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?
Hi monica,
command lines and grep will give you the answers.
fred
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.
You can create consensus from sam file and filter sequence based on your coordinate or align your genes to consensus.
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