Showing posts with label fasta. Show all posts
Showing posts with label fasta. Show all posts

Thursday, 31 March 2011

Convert SAM / BAM to fasta / fastq

Probably one of the most freq FAQ

latest thread in biostar
http://biostar.stackexchange.com/questions/6993/convert-bam-file-to-fasta-file

Samtofastq using Picard
http://picard.sourceforge.net/command-line-overview.shtml#SamToFastq

Samtools and awk to make fasta from sam
samtools view filename.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' - > filename.fasta
 
Biopython and pysam (code contributed by Brad Chapman)
http://biostar.stackexchange.com/questions/6993/convert-bam-file-to-fasta-file/6994#6994 

Friday, 11 June 2010

Yet another fasta splitter in perl

I love Miguel's explanation of bioinformatics "another way to torture biological data"
For me, I just massage them into the myriad of input formats that programs declare they require.. I never torture them!
Anyway to check out his variant on splitting fasta (I currently have python, csplit(linux), bioperl versions of fasta splitters)

Miguel's fasta splitter (into batches of fasta) requires BioPerl

Datanami, Woe be me