sRNA-seq Alignments - E5 Coral A.pulchra P.meandrina Using ShortStack on Mox

Steven had asked that I align the coral E5 sRNA-seq reads using ShortStack (GitHub Issue). I previously trimmed the sRNA-seq reads to 35bp in length (notebook). Next up was to actually perform the alignments using ShortStack4. A.pulchra was aligned to the P.millepora genome, per this GitHub Issue. This was run on Mox.

NOTE: Up to this point, I’ve processed all three species simultaneously for which we currently have sRNA-seq data: A.pulchra, P.evermanni, and P.meandrina. However, we currently haven’t decided on the canonical genome to use for P.evermanni (GitHub Issue), so P.evermanni is not included in this analysis.

Skip to RESULTS.

SLURM script (GitHub):

20230628-E5_coral-ShortStack-sRNAseq.sh

#!/bin/bash
## Job Name
#SBATCH --job-name=20230628-E5_coral-ShortStack-sRNAseq
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=10-00:00:00
## Memory per node
#SBATCH --mem=500G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq

### E5 sRNA-seq alignments using trimmed reads from 20230620 with ShortStack.

### Expects FastQ read directory paths to be formatted like:

# /gscratch/srlab/sam/data/P_meandrina/sRNAseq/trimmed

### Uses trimmed reads from 20230620. Expect FastQ filename format like:

# *flexbar_trim.20230621_[12]*.fastq.gz


###################################################################################
# These variables need to be set by user

## Assign Variables

# Set FastQ filename patterns
fastq_pattern='**flexbar_trim.20230621*.fastq.gz'

# Set number of CPUs to use
threads=40


# Input/output files
fastq_checksums=input_fastq_checksums.md5
sRNA_FastA="/gscratch/srlab/sam/data/miRBase/20230628-miRBase-mature.fa"

# Data directories
reads_dir=/gscratch/srlab/sam/data

## Inititalize arrays
trimmed_fastq_array=()



# Species array (must match directory name usage)
species_array=("A_pulchra" "P_meandrina")

# Programs associative array
declare -A programs_array
programs_array=(
    [ShortStack]="ShortStack"
    )

# Genomes associative array
declare -A genomes_array
genomes_array=(
    [A_pulchra]="/gscratch/srlab/sam/data/A_millepora/genomes/GCF_013753865.1_Amil_v2.1_genomic.fasta" \
    [P_meandrina]="/gscratch/srlab/sam/data/P_meandrina/genomes/Pocillopora_meandrina_HIv1.assembly.fasta"
    )


###################################################################################

# Exit script if any command fails
set -e

# Load Anaconda
# Uknown why this is needed, but Anaconda will not run if this line is not included.
. "/gscratch/srlab/programs/anaconda3/etc/profile.d/conda.sh"

# Activate flexbar environment
conda activate ShortStack4_env


# Set working directory
working_dir=$(pwd)

for species in "${species_array[@]}"
do
    ## Inititalize arrays
    trimmed_fastq_array=()


    echo "Creating ${species} directory ..." 

    mkdir --parents "${species}"

    # Change to species directory
    cd "${species}"


    # ShortStack output directory
    output_dir=$(pwd)

    echo "Now in ${PWD}."

    # Sync raw FastQ files to working directory
    echo ""
    echo "Transferring files via rsync..."

    rsync --archive --verbose \
    ${reads_dir}/${species}/sRNAseq/trimmed/${fastq_pattern} .

    echo ""
    echo "File transfer complete."
    echo ""

    ### Run ShortStack ###

    ### NOTE: Do NOT quote trimmed_fastq_list
    # Create array of trimmed FastQs
    trimmed_fastq_array=(${fastq_pattern})

    # Pass array contents to new variable as space-delimited list
    trimmed_fastq_list=$(echo "${trimmed_fastq_array[*]}")

    echo "Beginning ShortStack on ${species} sRNAseq using genome FastA:"
    echo "${genomes_array[${species}]}"
    echo ""

    ## Run ShortStack ##
    ${programs_array[ShortStack]} \
    --genomefile "${genomes_array[${species}]}" \
    --readfile ${trimmed_fastq_list} \
    --known_miRNAs ${sRNA_FastA} \
    --dn_mirna \
    --threads ${threads} \
    --outdir ${output_dir}/ShortStack_out

    echo "ShortStack on ${species} complete!"
    echo ""


    ######## Create MD5 checksums for raw FastQs ########

    for fastq in ${fastq_pattern}
    do
        echo "Generating checksum for ${fastq}"
        md5sum "${fastq}" | tee --append ${fastq_checksums}
        echo ""
    done

    ######## END MD5 CHECKSUMS ########

    ######## REMOVE INPUT FASTQS ########
    echo "Removing input FastQs."
    echo ""
    rm ${fastq_pattern}
    echo "Input FastQs removed."
    echo""

    echo "Now moving back to ${working_dir}."
    cd "${working_dir}"
    echo ""

done

####################################################################

# Capture program options
if [[ "${#programs_array[@]}" -gt 0 ]]; then
  echo "Logging program options..."
  for program in "${!programs_array[@]}"
  do
    {
    echo "Program options for ${program}: "
    echo ""
    # Handle samtools help menus
    if [[ "${program}" == "samtools_index" ]] \
    || [[ "${program}" == "samtools_sort" ]] \
    || [[ "${program}" == "samtools_view" ]]
    then
      ${programs_array[$program]}

    # Handle DIAMOND BLAST menu
    elif [[ "${program}" == "diamond" ]]; then
      ${programs_array[$program]} help

    # Handle NCBI BLASTx menu
    elif [[ "${program}" == "blastx" ]]; then
      ${programs_array[$program]} -help

    # Handle fastp menu
    elif [[ "${program}" == "fastp" ]]; then
      ${programs_array[$program]} --help
    else
    ${programs_array[$program]} -h
    fi
    echo ""
    echo ""
    echo "----------------------------------------------"
    echo ""
    echo ""
  } &>> program_options.log || true

    # If MultiQC is in programs_array, copy the config file to this directory.
    if [[ "${program}" == "multiqc" ]]; then
      cp --preserve ~/.multiqc_config.yaml multiqc_config.yaml
    fi
  done
fi


# Document programs in PATH (primarily for program version ID)
{
date
echo ""
echo "System PATH for $SLURM_JOB_ID"
echo ""
printf "%0.s-" {1..10}
echo "${PATH}" | tr : \\n
} >> system_path.log

RESULTS

Run time seemed relatively fast; just a bit over 4hrs:

Screencap showing ShortStack runtime on Mox of 4hrs 11mins 59secs

The results and links to various files are below. At this time, I have not done any evaluation of the results, nor have I looked into the ShortStack documentation to read how the results are formatted; will leave this for a future date and/or somebody else.

Output folder:

20230628-E5_coral-ShortStack-sRNAseq/

A.pulchra

Results files:

alignment_details.tsv (48K)
- MD5: d301b898b36c2022f22db538fa28b9eb

readfile	mapping_type	read_length	count
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	U	<21	120030
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	U	21	43333
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	U	22	105592
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	U	23	65039
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	U	24	84409
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	U	>24	3636233
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	P	<21	196501
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	P	21	61672
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	P	22	73193
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	P	23	69147
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	P	24	73631
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	P	>24	5674586
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	R	<21	25655
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	R	21	11222
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	R	22	12916
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	R	23	14482
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	R	24	19433
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	R	>24	1400108
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	H	<21	7685
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	H	21	2697
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	H	22	3260
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	H	23	3166
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	H	24	4394
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	H	>24	238409
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	N	<21	104184
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	N	21	60191
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	N	22	52988
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	N	23	59083
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	N	24	76366
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam	N	>24	5252357

Counts.txt (1.3M)
- MD5: 593069a45787e4176c5e17efe3b87d49

Coords	Name	MIRNA	sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1	sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_2	sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_1	sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_2	sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_1	sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_2	sRNA-ACR-173-S1-TP2.flexbar_trim.20230621_1	sRNA-ACR-173-S1-TP2.flexbar_trim.20230621_2	sRNA-ACR-178-S1-TP2.flexbar_trim.20230621_1	sRNA-ACR-178-S1-TP2.flexbar_trim.20230621_2
NC_058066.1:152483-152906	Cluster_1	N	1	3	126	137	1	2	2	2	2	3
NC_058066.1:161082-161790	Cluster_2	N	46	57	48	54	210	319	33	25	190	270
NC_058066.1:203244-203650	Cluster_3	N	17	15	37	30	11	15	15	10	41	33
NC_058066.1:204535-205150	Cluster_4	N	6	6	270	254	18	16	12	6	56	59
NC_058066.1:205746-206966	Cluster_5	N	82	93	450	453	66	71	253	239	239	127
NC_058066.1:210855-211344	Cluster_6	N	340	351	213	210	83	81	0	1	656	647
NC_058066.1:349656-351297	Cluster_7	N	497	510	1246	1247	841	772	768	762	19	21
NC_058066.1:351491-353439	Cluster_8	N	3253	3186	2069	2014	2158	2159	2113	2084	169	174
NC_058066.1:776275-776779	Cluster_9	N	0	0	318	280	10	11	58	61	180	175

Results.txt (2.8M)
- MD5: 0ae9d3267579e8614e57a73a3490430d

Locus	Name	Chrom	Start	End	Length	Reads	UniqueReads	FracTop	Strand	MajorRNA	MajorRNAReads	Short	Long	21	22	23	24	DicerCall	MIRNA	known_miRNAs
NC_058066.1:152483-152906	Cluster_1	NC_058066.1	152483	152906	424	279	77	0.512544802867383	.	UAAGUACUUUAUCAACUAACUCUAGGCA	77	3	260	0	3	0	13	N	N	NA
NC_058066.1:161082-161790	Cluster_2	NC_058066.1	161082	161790	709	1252	475	0.623801916932907	.	AGUCGACGAAUUUGCCAUGAAGCUAGUA	71	39	1129	26	10	5	43	N	N	NA
NC_058066.1:203244-203650	Cluster_3	NC_058066.1	203244	203650	407	224	112	0.535714285714286	.	UUCUGACUCUAUUAGCAACGAAGACUUU	38	2	217	2	1	0	2	N	N	NA
NC_058066.1:204535-205150	Cluster_4	NC_058066.1	204535	205150	616	703	343	0.500711237553343	.	UCCCAACACGUCUAGACUGUACAAUUUCU	33	4	682	2	0	7	8	N	N	NA
NC_058066.1:205746-206966	Cluster_5	NC_058066.1	205746	206966	1221	2073	732	0.535455861070912	.	CAAAAGAGCGGACAAAAUAGUCGACAGAUU	152	15	1999	8	6	13	32	N	N	NA
NC_058066.1:210855-211344	Cluster_6	NC_058066.1	210855	211344	490	2582	667	0.497676219984508	.	UAAUACUUGUAGUGAAGGUUCAAUCUCGA	97	17	2355	13	18	39	140	N	N	NA
NC_058066.1:349656-351297	Cluster_7	NC_058066.1	349656	351297	1642	6683	2375	0.501571150680832	.	UCAGCUUGGAAAUGACAGCUUUUGACGU	294	53	6417	22	45	44	102	N	N	NA
NC_058066.1:351491-353439	Cluster_8	NC_058066.1	351491	353439	1949	19379	3490	0.498632540378761	.	UUUCAAAUCAAAGAUCUUCGCAACGAUGA	1115	135	18526	59	101	247	311	N	N	NA
NC_058066.1:776275-776779	Cluster_9	NC_058066.1	776275	776779	505	1093	284	0.517840805123513	.	UGUUAUUGUCUUUGAGUGCCCAAAUGUGU	64	3	1080	2	3	2	3	N	N	NA

GFFs:
- Results.gff3 (1.8M)
  - MD5: 84be69fd3fc4a02fd64c83ad0cbdaa63
- known_miRNAs.gff3 (88K)
  - MD5: d9c407fde49dad766805eed720ef56b0
BAMs:
- merged_alignments.bam (3.2G)
  - MD5: 6cdc0a903f5761528518453c5cf735c4
- sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.bam (301M)
  - MD5: 519cb501a0f5fa32539d3571c9017929
- sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_2.bam (307M)
  - MD5: 4b01b68a60ae5563c1dbada3eae9cde9
- sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_1.bam (337M)
  - MD5: 3347abd91870d380d719281e091571a0
- sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_2.bam (340M)
  - MD5: 056895a4d142c5c0bc0cd0ea52f866a7
- sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_1.bam (358M)
  - MD5: 968fcf9472f4d9da500878a7bc4d4e87

P.meandrina

Results files:

Counts.txt (684K)

MD5: 45c7fa265a74c685ce60848447fa4566

Coords	Name	MIRNA	sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1	sRNA-POC-47-S1-TP2.flexbar_trim.20230621_2	sRNA-POC-48-S1-TP2.flexbar_trim.20230621_1	sRNA-POC-48-S1-TP2.flexbar_trim.20230621_2	sRNA-POC-50-S1-TP2.flexbar_trim.20230621_1	sRNA-POC-50-S1-TP2.flexbar_trim.20230621_2	sRNA-POC-53-S1-TP2.flexbar_trim.20230621_1	sRNA-POC-53-S1-TP2.flexbar_trim.20230621_2	sRNA-POC-57-S1-TP2.flexbar_trim.20230621_1	sRNA-POC-57-S1-TP2.flexbar_trim.20230621_2
Pocillopora_meandrina_HIv1___Sc0000000:9091-9526	Cluster_1	N	1828	1784	1393	1412	1842	1812	3219	3286	3565	3477
Pocillopora_meandrina_HIv1___Sc0000000:53578-53997	Cluster_2	N	24	24	52	53	67	67	53	55	95	91
Pocillopora_meandrina_HIv1___Sc0000000:146768-147202	Cluster_3	N	3	248	2	73	0	116	0	107	5	226
Pocillopora_meandrina_HIv1___Sc0000000:150243-150718	Cluster_4	N	437	422	691	676	813	804	692	700	1021	1007
Pocillopora_meandrina_HIv1___Sc0000000:173728-174150	Cluster_5	N	171	167	169	167	269	271	317	318	336	334
Pocillopora_meandrina_HIv1___Sc0000000:187648-188072	Cluster_6	N	8	7	16	13	28	27	59	72	76	76
Pocillopora_meandrina_HIv1___Sc0000000:485727-486254	Cluster_7	N	114	112	98	96	49	50	165	168	270	259
Pocillopora_meandrina_HIv1___Sc0000000:525310-527341	Cluster_8	N	3753	3707	1260	1254	4711	4627	2811	2878	2607	2572
Pocillopora_meandrina_HIv1___Sc0000000:541262-541723	Cluster_9	N	127	130	86	91	85	96	331	317	85	87

Results.txt (1.4M)

MD5: 7b96db202d049a53f154ee3fc1fcda08

Locus	Name	Chrom	Start	End	Length	Reads	UniqueReads	FracTop	Strand	MajorRNA	MajorRNAReads	Short	Long	21	22	23	24	DicerCall	MIRNA	known_miRNAs
Pocillopora_meandrina_HIv1___Sc0000000:9091-9526	Cluster_1	Pocillopora_meandrina_HIv1___Sc0000000	9091	9526	436	23618	903	0.501566601744432	.	UCUACCACUGAGCUAUACCCCC	3810	2853	9677	1223	8614	359	892	N	N	NA
Pocillopora_meandrina_HIv1___Sc0000000:53578-53997	Cluster_2	Pocillopora_meandrina_HIv1___Sc0000000	53578	53997	420	581	27	0.500860585197935	.	GCCUAAGUUGCUUGGAACA	142	577	4	0	0	0	0	N	N	NA
Pocillopora_meandrina_HIv1___Sc0000000:146768-147202	Cluster_3	Pocillopora_meandrina_HIv1___Sc0000000	146768	147202	435	780	108	0.971794871794872	+	AGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	267	2	773	4	0	1	0	N	N	NA
Pocillopora_meandrina_HIv1___Sc0000000:150243-150718	Cluster_4	Pocillopora_meandrina_HIv1___Sc0000000	150243	150718	476	7263	645	0.496902106567534	.	UUAUGUGAUGAGUAUGUUAAUGUACUCUCUGAGC	566	1692	2932	1272	749	280	338	N	N	NA
Pocillopora_meandrina_HIv1___Sc0000000:173728-174150	Cluster_5	Pocillopora_meandrina_HIv1___Sc0000000	173728	174150	423	2519	134	0.500992457324335	.	CAACCAGAUCACAGCAAUCAAA	438	212	8	83	1269	887	60	22	N	NA
Pocillopora_meandrina_HIv1___Sc0000000:187648-188072	Cluster_6	Pocillopora_meandrina_HIv1___Sc0000000	187648	188072	425	382	74	0.523560209424084	.	AUAAAUGUCACUACAAGAAACCUGAAAUCGU	25	1	366	2	2	4	7	N	N	NA
Pocillopora_meandrina_HIv1___Sc0000000:485727-486254	Cluster_7	Pocillopora_meandrina_HIv1___Sc0000000	485727	486254	528	1381	391	0.503982621288921	.	UUGCACUAGAACAGACUGUGCUUCCAUAUCAGCUG	152	132	1174	14	22	6	33	N	N	NA
Pocillopora_meandrina_HIv1___Sc0000000:525310-527341	Cluster_8	Pocillopora_meandrina_HIv1___Sc0000000	525310	527341	2032	30180	6208	0.498939695162359	.	UUUUCGUCACUUUCUUCAGCCUCAGAGU	973	277	27960	102	211	625	1005	N	N	NA
Pocillopora_meandrina_HIv1___Sc0000000:541262-541723	Cluster_9	Pocillopora_meandrina_HIv1___Sc0000000	541262	541723	462	1435	283	0.500348432055749	.	UUGGACGAAAUUUCGAGGUUCACACUCGUU	86	0	1425	0	7	2	1	N	N	NA

alignment_details.tsv (48K)

MD5: b89a4d5f7d1c49fcc8b3c31fdb316837

readfile	mapping_type	read_length	count
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	U	<21	277334
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	U	21	114752
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	U	22	331234
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	U	23	133358
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	U	24	46856
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	U	>24	1441069
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	P	<21	472110
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	P	21	109577
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	P	22	119506
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	P	23	96527
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	P	24	73770
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	P	>24	3922569
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	R	<21	270975
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	R	21	95814
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	R	22	130073
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	R	23	82638
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	R	24	190938
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	R	>24	1254706
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	H	<21	20811
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	H	21	5811
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	H	22	5117
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	H	23	5552
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	H	24	5909
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	H	>24	47393
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	N	<21	122944
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	N	21	59503
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	N	22	101407
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	N	23	92953
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	N	24	117111
/gscratch/scrubbed/samwhite/outputs/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam	N	>24	5315658

GFFs:
- Results.gff3 (860K)
  - MD5: 6dde17bf837ca3ee56534fb638a655cf
- known_miRNAs.gff3 (160K)
BAMs:
- merged_alignments.bam (2.5G)
  - MD5: a8fe8903ee2690b925768c205ef88692
- sRNA-POC-47-S1-TP2.flexbar_trim.20230621_1.bam (227M)
  - MD5: 0d411052dc3a4b0ffe05dbe2dc695e27
- sRNA-POC-47-S1-TP2.flexbar_trim.20230621_2.bam (232M)
  - MD5: b9450ad15e29061565516d079a77e111
- sRNA-POC-48-S1-TP2.flexbar_trim.20230621_1.bam (236M)
  - MD5: 09c05641624ce2f26cec91df6ab2e51d
- sRNA-POC-48-S1-TP2.flexbar_trim.20230621_2.bam (240M)
  - MD5: a0c4cf038cc37be46c863c2be831b00c
- sRNA-POC-50-S1-TP2.flexbar_trim.20230621_1.bam (220M)
  - MD5: 347284e0c5b0fa8f049a26a075f8b82a
- sRNA-POC-50-S1-TP2.flexbar_trim.20230621_2.bam (222M)
  - MD5: 2c3fb0d9d557c572f4bd10541d56f603
- sRNA-POC-53-S1-TP2.flexbar_trim.20230621_1.bam (282M)
  - MD5: cd31c3f587e4e6aa13acb00fd2fe67a3
- sRNA-POC-53-S1-TP2.flexbar_trim.20230621_2.bam (278M)
  - MD5: f09c6a03df26536d90c7f80262911d3a
- sRNA-POC-57-S1-TP2.flexbar_trim.20230621_1.bam (255M)
  - MD5: b55a29681e8979e09486c2abc16c492f
- sRNA-POC-57-S1-TP2.flexbar_trim.20230621_2.bam (259M)
  - MD5: 26e92bb5edec78b2d613065a52272ea0

RESULTS

A.pulchra

Results files:

GFFs:

BAMs:

P.meandrina

Results files:

GFFs:

BAMs: