Files for IGV
Min length 10,000
#winning
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QPX
TE, repeats…
./RepeatProteinMask /Volumes/Bay3/Software/trf_data/in/QPX_v015.fasta
Masking Simple and Low Complexity Repeats...
- TRF : 981
- RepeatMasker: 0
./RepeatMasker -dir /Volumes/Bay3/Software/RepeatMasker/out -gff /Volumes/Bay3/Software/trf_data/in/QPX_v015.fasta
RepeatMasker version open-3.3.0
Search Engine: NCBI/RMBLAST
Master RepeatMasker Database: /Volumes/Bay3/Software/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: 20120418 )
analyzing file /Volumes/Bay3/Software/trf_data/in/QPX_v015.fasta
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Idea : grab fasta from transcriptome overlap.. ID snps (too much)
Get each RNAseq track on Genome
Do RNA-Seq in CLC - export---
RUnning on GreenBird.
Exported as SAM, now bed tools
eported as BAM
made beds….
Next will do genome coverage using these beds… probably using split?
too big
maybe genome coverage
./genomeCoverageBed
bedtools genomecov [OPTIONS] -i <bed/gff/vcf> -g <genome>./
./genomeCoverageBed -i /Volumes/web/cnidarian/QPX_RT_bamtobed_B_split.bed -g /Volumes/web/cnidarian/QPX_browser/QPX_v017.fasta > /Volumes/web/cnidarian/QPX_genomeCov_RTsplit.bed
nope
(1) The genome file should tab delimited and structured as follows:
<chromName><TAB><chromSize>
For example, Human (hg19):
chr1 249250621
chr2 243199373
…
robertsmac:emboss sr320$ ./infoseq /Volumes/web/cnidarian/QPX_browser/QPX_v017.fasta -only -name -length > /Volumes/web/cnidarian/QPX_browser/QPX_v017_length
Display basic information about sequences
./genomeCoverageBed -i /Volumes/web/cnidarian/QPX_RT_bamtobed_B_split.bed -g /Volumes/web/cnidarian/QPX_browser/QPX_v017_length > /Volumes/web/cnidarian/QPX_genomeCov_RTsplit.bed
./genomeCoverageBed -bg -i /Volumes/web/cnidarian/QPX_RT_bamtobed_B_split.bed -g /Volumes/web/cnidarian/QPX_browser/QPX_v017_length > /Volumes/web/cnidarian/QPX_genomeCov_RTsplitB.bedgraph
./genomeCoverageBed -bg -i /Volumes/web/cnidarian/QPX_10_bamtobed_B_split.bed -g /Volumes/web/cnidarian/QPX_browser/QPX_v017_length > /Volumes/web/cnidarian/QPX_genomeCov_10splitB.bedgraph
Lets go straight from BAM
./genomeCoverageBed -split -bg -ibam /Volumes/web/cnidarian/filtered_QPX_ATCC_10C_CGTACG_L001_R1RNAseq.bam -g /Volumes/web/cnidarian/QPX_browser/QPX_v017_length > /Volumes/web/cnidarian/QPX_genomeCov_10_bam.bedgraph
./genomeCoverageBed -split -bg -ibam /Volumes/web/cnidarian/filtered_QPX_ATCC_RT_GAGTGG_L001_R1RNAseq.bam -g /Volumes/web/cnidarian/QPX_browser/QPX_v017_length > /Volumes/web/cnidarian/QPX_genomeCov_RT_bam.bedgraph
Decided on v01.7 as scaffold…..
genomic SNPs from v01.5 (will change prefix)
blastn of transcriptome
SP tblastn
SP tblastn v017; evalue 1E-40 -max_target_seqs 2
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Physio3AA
Physo3AA tblastn to v017; -evalue 1E-40 -max_target_seqs 10
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CG location