sam formate issue

Question

[Azhar]

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?

[David Langenberger]

Perhaps it might help, if you post your call?

[Azhar]

I did that but it says no file specified

[Devon Ryan]

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.

Answer 1

[Devon Ryan]

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

[Azhar]

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

[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

[Devon Ryan]

Please post this as a new question.

[Azhar]

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