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seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
My in.fastq file is this:
@A00869:294:HCW57DSXY:2:1101:3929:1000 1:N:0:ACTGGACA+ACTGGACA
GCCACTCTGGCTATGTGAATACGGTGGCGGTGTCGCCTGATGGGTCGCTTTGCGCGAGCGGAGGGAAAGATGGGACTATTTTGTTGTGGGACTTGTCGGAGGGCAAGAGGCTTTACTCGCTCGATGCTGGCTCGATCATTAATGCTCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF
@A00869:294:HCW57DSXY:2:1101:5882:1000 1:N:0:ACTGGACA+ACTGGACA
TTTTGCCTAGTTTCTTCATTGTTGGGTCGTTTCACAACTCATGCTGTTGGGTCGGAGGCTATTGGGATTCTTGTGAATTTCGATCTCAATTCGGAATCGATAACCAATTTGATGCAACCTGCGAAGGTATCGTTAATGGTGGACATGTT
+
FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
My ID list is this:
A00869:294:HCW57DSXY:2:1101:3929:1000 1:N:0:ACTGGACA+ACTGGACA
A00869:294:HCW57DSXY:2:1101:5882:1000 1:N:0:ACTGGACA+ACTGGACA
A00869:294:HCW57DSXY:2:1101:5882:1000 1:N:0:ACTGGACA+ACTGGACA
I am using the above subject command correctly but the output file does not contain the full sequence. The output file sequence contains like this:
@A00869:294:HCW57DSXY:2:1101:3929:1000 1:N:0:ACTGGACA+ACTGGACA
A
+
F
@A00869:294:HCW57DSXY:2:1101:5882:1000 1:N:0:ACTGGACA+ACTGGACA
A
+
F
@A00869:294:HCW57DSXY:2:1101:5882:1000 1:N:0:ACTGGACA+ACTGGACA
T
+
F
Anyone can explain why output file not containing the full sequence but only one basepair with each ID?
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GenoMax
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KHURRAM SHAHZAD •
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KHURRAM SHAHZAD •
1 answer
Use everything before the whitespace in list.txt, for example A00869:294:HCW57DSXY:2:1101:3929:1000 and not A00869:294:HCW57DSXY:2:1101:3929:1000 1:N:0:ACTGGACA+ACTGGACA.
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