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sam formate issue

I am using makeTagDirectory command to get peaks by using findpeaks.pl by Homer, but when I run makeTagDirectory command it says

!!! Couldn't recognize: -formate !!!

whereas the file is bowtie2 output sam formate and I check it by opening in bash it is in sam formate

What could be the issue?

chip-seq
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updated by Ram Ram • written by Azhar • Azhar

Perhaps it might help, if you post your call?

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updated by Ram Ram • written by David Langenberger David Langenberger

I did that but it says no file specified

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updated by Ram Ram • written by Azhar • Azhar

Then presumably you didn't specify a file...

Try posting the actual command that you're typing, it prevents us from needing to read your mind.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

1 answer

If you correctly spell "format" the error will likely go away.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

Thanks a lot I have run maketag and find peaks successfully but how to view results because I only used

findPeaks <tag directory>

out of

findPeaks <tag directory> -style <factor|histone|groseq> -o auto -i <control tag directory>

and it showed some results on bash line

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updated by Ram Ram • written by Azhar • Azhar

Dear I am using Homer you can help. I try to find out Enhancers by using -typical command option but it does not works and produce same simple peak file produced by find peaks whereas -style super works good for super Enhancers

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updated by Ram Ram • written by Azhar • Azhar

Please post this as a new question.

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written by Devon Ryan Devon Ryan

I have done with tittle Enhcar you can see, and help

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written by Azhar • Azhar

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