User: Chris Penkett

gravatar for Chris Penkett
Chris Penkett480
Reputation:
480
Status:
New User
Location:
Cambridge, UK
Website:
http://biostar.stackex...
Last seen:
7 years, 3 months ago
Joined:
9 years, 1 month ago
Email:
c************@yahoo.com

Posts by Chris Penkett

<prev • 47 results • page 1 of 5 • next >
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Answer: A: How To Get Number Of Reads In Bam File Efficiently In Python?
... Short python/pysam answer: import pysam filename = 'test.bam' print reduce(lambda x, y: x + y, [ eval('+'.join(l.rstrip('\n').split('\t')[2:]) ) for l in pysam.idxstats(filename) ]) ...
written 7.3 years ago by Chris Penkett480 • updated 13 months ago by RamRS24k
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4
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Answer: A: Emacs Bioinformatics - Ale Vs Biomode Vs Ralee
... [This post](/p/14840/) also suggests ralee with one comment saying it looked good. ...
written 7.8 years ago by Chris Penkett480 • updated 4 weeks ago by RamRS24k
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Comment: C: How To Pull Out Qual From Multi Line Fastq?
... line[0] can be '+' for one of the qual lines if the phred33 score is 10. So maybe this code may break in some cases. ...
written 7.9 years ago by Chris Penkett480
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Comment: C: How To Pull Out Qual From Multi Line Fastq?
... line[0] can be '+' for one of the qual lines if the phred33 score is 10. So maybe this code may break in some cases. 0 1 2 3 4 01234567890123456789012345678901234567890 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI ...
written 7.9 years ago by Chris Penkett480
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Answer: A: Seq Qc/Trimming Code Preferences?
... RNA-SeQC is a new Broad tool to do visual QC for RNA-seq data. ...
written 7.9 years ago by Chris Penkett480
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Comment: C: Getting Unmapped Reads: Comparing Fastq To Bam
... TopHat only puts in the mapped reads - it'll put them in multiple times if they map to many locations as well - so you may need to pipe column 1 into sort/uniq UNIX pipes to get unique mapped read names. ...
written 7.9 years ago by Chris Penkett480
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Comment: C: Rna-Seq Paired-End Samtools Script
... Are you sure you want to run mpileup on the data - do you want SNP's/indels or per-base sequencing depth for an RNA-seq dataset? ...
written 7.9 years ago by Chris Penkett480
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Comment: C: Igv Dbsnp Version "1.3.1"
... Typo? - they spell skeletal wrong in the Bodymap data for hg19. ...
written 7.9 years ago by Chris Penkett480
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Answer: A: Removal Of Low Quality Reads With Trailing "B"
... Filter the CIGARs for these dodgy reads and look at the base qualities: samtools view out.bam | perl -F"\t" -ane 'print "$F[5]\t$F[10]\n" if $F[5] =~ /[7-9][0-9]S/' > test.txt I've only got 76bp data to hand, so my CIGAR needs a different reg-ex: samtools view out.bam | perl -F"\t" -ane 'print " ...
written 7.9 years ago by Chris Penkett480
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Comment: C: Matching Complementary Regions Of 2 Dna Sequences
... SW will not make the gaps needed in this case unless you can penalise them less. Perhaps increase the match values from 1 to something larger and reduce the gap open and extension penalties. ...
written 7.9 years ago by Chris Penkett480

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