I was attempting the tutorial and got all the way through to parsing with FIMO the sequences within the peaks that match the PWM. However when I entered the command:
I received back the following message many times over, seemingly for all of the contents:
Warning: ? is not a valid character in DNA alphabet.
Converting ? to N.
Once I entered zcat $sites | head to look at the sites it just gave back the header,
pattern name sequence name start stop strand score p-value q-value matched sequence
The only other issue I encountered is at an earlier step where I was informed that hg19.fa did not have an index file associated with it so I used samtools faidx to create one. I am not sure if this led to the later issues.
I followed the tutorial exactly, using all of the same files. If there are any thoughts on what may have happened it would really be appreciated, thank you.
Hi,
I was attempting the tutorial and got all the way through to parsing with FIMO the sequences within the peaks that match the PWM. However when I entered the command:
I received back the following message many times over, seemingly for all of the contents:
Warning: ? is not a valid character in DNA alphabet. Converting ? to N.
Once I entered zcat $sites | head to look at the sites it just gave back the header,
pattern name sequence name start stop strand score p-value q-value matched sequence
The only other issue I encountered is at an earlier step where I was informed that hg19.fa did not have an index file associated with it so I used samtools faidx to create one. I am not sure if this led to the later issues.
I followed the tutorial exactly, using all of the same files. If there are any thoughts on what may have happened it would really be appreciated, thank you.
Rob.