How to identify the presence of genes in sam file?

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Frederic Lepretre

Hi monica,

command lines and grep will give you the answers.

fred

Monica Steffi Matchado

Hi Frederic

Could you please give one example how to get a list of genes

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.

Sureshkumar v.

You can create consensus from sam file and filter sequence based on your coordinate or align your genes to consensus.