I have two samfiles which were generated by bowtie. I have set of gene sequences separately in fasta format. I need to check whether these set of genes are present in sam files or not. How can I achieve this?
Monica Steffi Matchado
Hi Frederic
Could you please give one example how to get a list of genes
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Frederic Lepretre
on commande lines, redirect your position in the right folder where you'll have the sam file, and type :
egrep "sequence1|sequence2|sequence3|sequence4" file.sam > results.bed
the results.bed file will be created in this last folder.
fred
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Sureshkumar v.
You can create consensus from sam file and filter sequence based on your coordinate or align your genes to consensus.
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