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lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats
MIT License
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Retriving fastq but no result #105

Closed aungthurhahein closed 6 years ago

aungthurhahein commented 6 years ago

I was trying to get subsequences but the result doesn't show up anything.

ID File:

@NB501274:11:HG3WCAFXX:1:11101:10000:11203
@NB501274:11:HG3WCAFXX:1:11101:10000:8239
@NB501274:11:HG3WCAFXX:1:11101:10001:15495

Orginial Fastq file:

 @NB501274:11:HG3WCAFXX:1:11101:16414:1046 1:N:0:ATCACG
TAAGCTAATGCCGGTGTAAAGTGTTGAGTCCCTTAGTCAATCTCCAAGAGCCGTGTAGCCCTGAACTGGGGTCCC
+
AAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEEEEAE
@NB501274:11:HG3WCAFXX:1:11101:13913:1047 1:N:0:ATCACG
GGCAAACGTCTTCGCCGAGGTGACACACCGAAGAAGCCCAATCGCAGTAGTAGCTCTGGGGGTTGTACAGCGTTC
+
AAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEE
@NB501274:11:HG3WCAFXX:1:11101:13331:1048 1:N:0:ATCACG
TGGAGAACGATGCGGCCACCTCGCTTGTTCTGGTACTTCATGAAAATCTGGGCATGTTCCCTTTCCTCATCGCTC
+
AAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEE
@NB501274:11:HG3WCAFXX:1:11101:11057:1049 1:N:0:ATCACG
GCCTGTGGTATCCAGGTAGGTGTAGTGCAGACTGTCAGCTTTGCGCTCTACTGGGTATGGTGTCTCAAGATCAAT
+

CMD: seqtk subseq R1.fq test.lst

shenwei356 commented 6 years ago

Remove @ in ID file.

sed 's/^@//' id.txt > new.txt
lh3 commented 6 years ago

Thanks, @shenwei356!

To @aungthurhahein: as @shenwei356 said, you need to remove the leading @ character.