Entering edit mode
5.7 years ago
kalanir
•
0
When I run the seqtk subseq to extract sequences, it completely disregards the quality scores and the sequence.
>>>./seqtk subseq file.fastq IDs.txt
@NS500126:798:HWTLTAFXX:1:11101:10771:1083:1-1 1:N:0:AATGGTCG+NGACCATT
G
+
A
@NS500126:798:HWTLTAFXX:1:11101:2195:1084:1-1 1:N:0:AATGGTCG+NGACCATT
G
+
A
@NS500126:798:HWTLTAFXX:1:11101:2581:1084:1-1 1:N:0:AATGGTCG+NGACCATT
T
+
A
It's pulling the first character in the quality score and read; however, it's not pulling the full line.
Is there a way to fix that?
As per seqtk results, remove spaces in sequence header in fastq file and ids.txt and try again.
try seqkit:
The command you provided worked!! Though I'm not sure why you suggested I remove spaces.
can you show us the output of
It doesn't seem to output anything.
if I look at the first couple lines of
file.fastq
it looks like this:This header in original post
does not match the example posted above
What gives?