FISH546 Module 3 - de novo assembly

https://docs.google.com/spreadsheet/ccc?key=0AtV_gF766XZAdEVVOUpNMmJHN1RjUjVud3dtRjdwOWc#gid=0

./Trinity.pl --seqType fq --JM 20000G --left /Volumes/web/whale/fish546/module3_assembly/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz --right /Volumes/web/whale/fish546/module3_assembly/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz --CPU 10 --output /Volumes/web/whale/fish546/module3_assembly

./Trinity.pl --seqType fq --JM 20000G --left /fish546/module3_assembly/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz --right /fish546/module3_assembly/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz --CPU 10 --output /fish546/module3_assembly

Writing out to NAS creating 60GB Temp file the crashed computer.

Working if local…???

./velveth /Volumes/web/whale/ 21 -fastq -short /Volumes/web/cnidarian/Olurida_trans_v2_trimmed%20libraries.fastq

robertsmac:velvet_1.1.07 sr320$ ./velveth /Volumes/web/whale/fish546/module3_assembly/ 21 -fastq -short /Volumes/web/whale/fish546/module3_assembly/SE_sm_filtered_LTL_PS63_AGTTCC_L005_R1.fastq

[0.000001] Reading FastQ file /Volumes/web/whale/fish546/module3_assembly/SE_sm_filtered_LTL_PS63_AGTTCC_L005_R1.fastq

No luck

……..

SOAP

genefish:soap Steven$ ./SOAPdenovo31mer all -s config -o fish546mod3

Version 1.05: released on July 29th, 2010

pregraph -s config -o fish546mod3

In config, 1 libs, max seq len 75, max name len 256

8 thread created

read from file:

filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz

read from file:

filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz

time spent on hash reads: 367s, 79646478 reads processed

[LIB] 0, avg_ins 200, reverse 0

368302795 nodes allocated, 4221263334 kmer in reads, 4221263334 kmer processed

338341102 linear nodes

time spent on marking linear nodes 3s

time spent on pre-graph construction: 370s

deLowKmer 0, deLowEdge 1

Start to remove tips of single frequency kmers short than 46

9357683 tips off

8 thread created

5256794 linear nodes

Start to remove tips which don't contribute the most links

kmer set 0 done

kmer set 1 done

kmer set 2 done

kmer set 3 done

kmer set 4 done

kmer set 5 done

kmer set 6 done

kmer set 7 done

820766 tips off

8 thread created

0 linear nodes

time spent on cutTipe: 143s

Completed in ~Hour

Complete files (input, config, file, output) available @

http://eagle.fish.washington.edu/whale/index.php?dir=fish546%2Fmodule3_assembly%2FSOAP_mod3_PE%2F

filtering contig output

Ran compute sequence length in Galaxy

Histogram of sequence length

XY Length and Coverage

Summary Statistics on Length (galaxy)

#sum	mean	stdev	0%	25%	50%	75%	100%
2.2802e+07	688.965	360.703	400	464	566	776	5823

L (logsscale) v coverage

CONFIG

max_rd_len=75
[LIB]
avg_ins=200
reverse_seq=0
asm_flags=3
rank=
q1=filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz
q2=filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz
[LIB]
avg_ins=
reverse_seq=0
asm_flags=3
rank=
q1=
q2=
[LIB]
avg_ins=--reverse_seqs3=0
reverse_seq=
asm_flags=3
rank=
q1=
q2=

37,082 at 400bp minimum

#sum	mean	stdev	0%	25%	50%	75%	100%
3.15707e+07	851.376	603.753	400	491	644	977	10274

Going to assume Unitig file is final output

25,028 sequences min 400

#sum	mean	stdev	0%	25%	50%	75%	100%
2.75774e+07	1101.86	884.089	400	546	797	1332	18616

d-128-95-149-219:bin sr320$ ./blastx -query /Volumes/web/whale/fish546/blast/query/fish546_module_3_Abyss_iplant_contigs.fa -db /Volumes/web/whale/fish546/blast/db/nr -out /Volumes/web/whale/fish546/blast/out/fish546_PEAbyss_NR.xml -outfmt 5 -max_target_seqs 1 -num_threads 8

./blastx -query /Volumes/web/whale/fish546/blast/query/fish546_module_3_Abyss_iplant_contigs.fa -db /Volumes/web/whale/fish546/blast/db/swissprot -out /Volumes/web/whale/fish546/blast/out/fish546_PEAbyss_swissprot.xml -outfmt 5 -max_target_seqs 1 -num_threads 8

41,319 sequences 400bp

#sum	mean	stdev	0%	25%	50%	75%	100%
4.63808e+07	1122.51	984.788	400	526	768	1336	19213

Trying Abyss on Iplant again - changing kmer to 40…

33,877 contigs minimum 400 bp

#sum	mean	stdev	0%	25%	50%	75%	100%
4.50732e+07	1330.5	1272.28	401	545	858	1627	18596