seqtk subseq command not pulling full fastq reads
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?
1 answer
That is because there is a whitespace in the header of the fastq.
@NS500126:798:HWTLTAFXX:1:11101:10771:1083:1-1 1:N:0:AATGGTCG+NGACCATT
Only the part before "1:N:0:AATGGTCG+NGACCATT" is the fastq name, the rest is not.
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can you show us the output of
It doesn't seem to output anything.
if I look at the first couple lines of
file.fastqit looks like this:This header in original post
does not match the example posted above
What gives?
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.