BBmap bbduk.sh for filtering reads

Question

[kinase]

I'm looking to filter reads that contain a stretch of A's, I found these posts looking for polyA tails, meaning this should work all the same (Identify RNA-seq reads containing polyA sequence, Identifying RNA-seq reads containing polyA stretch). However, I cannot get it to work. Given just these two reads, the first of which does contain a stretch of 8 A's and the second of which does not, what is the correct command to separate the first from the second?

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@A01587:190:GW220612000:1:2101:6090:1016 1:N:0:AATCCAGC+CTAGTCGA
NATTTGAATTCAGAACCGCTTCTGCTCAATTAGAAGGTGGTGTCCATAATTTGCACTCCTATGAAAAACGTCTATACAATTGAGTAAGCATCCATAGATATTTAAAAGTTTATTTTTGCATATAAATATACCTTCATAGAGATCAACAAAACTAAAATAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTATCTGTTATTATTTGATGCTTTAACCAAAGGATATTGGACCAAGTCAAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFF,:,,,,::,,,,F,:,FF,::,F:,:::,::F,,,,:FF,,,F,F:,,F,FF
@A01587:190:GW220612000:1:2101:27850:1031 1:N:0:AATCCAGC+CTAGTCGA
CTAAAGCCTTTTTGTAATCCAATGGAGCAGCACTCATCGTAAAATGTTTGTTAGGTTTCTTCAAAGCTATGGAATTGGTCCAATATCCTTTGGTTCAAGCAGCAAAGAAGACCAGAGAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAATATTATATTTTTATTTTTTTTTTTTTGTTTATAAATTTTTTTTTGTTTTTGTATTTTGTTTGATAATTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF,F:,:,:,F,::,,,,,FF,F,,,:,,,,,,,,,,,,,,,,,,,,:,F,:,::,,FF::,:,,,,,,,,:,:,,,,,,,

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My expectation was that this would work but it just sends both reads to a file

bbduk.sh -in=in.fq.gz -outm=outm.fq.gz -literal=AAAAAAAA

Other non-functioning attempts include

bbduk.sh -in=in.fq.gz -out=out.fq.gz -outm=outm.fq.gz -literal=AAAAAAAA
bbduk.sh -in=in.fq.gz -out=out.fq.gz -outm=outm.fq.gz -literal=AAAAAAAA -k=3
bbduk.sh -in=in.fq.gz -out=out.fq.gz -literal=AAAAAAAA
bbduk.sh -in=in.fq.gz -outm=outm.fq.gz -literal=AAAAAAAA -k=3

I suppose another option is to use cutadapt and tell it the adapter is a bunch of A's and simply pass those reads to a file, but I'd still like to know what I'm doing wrong here.

Answer 1

[GenoMax]

There is no - in front of BBtools options. So the command would be following (turn off rev complementing to not match polyT's).

$ bbduk.sh -Xmx2g in=test.fq outm=stdout.fq literal=AAAAAAAA k=4 rcomp=f

0.022 seconds.
Initial:
Memory: max=2058m, total=2058m, free=2015m, used=43m

Added 4 kmers; time:    0.003 seconds.
Memory: max=2058m, total=2058m, free=2004m, used=54m

Input is being processed as unpaired
Started output streams: 0.017 seconds.
@A01587:190:GW220612000:1:2101:6090:1016 1:N:0:AATCCAGC+CTAGTCGA
NATTTGAATTCAGAACCGCTTCTGCTCAATTAGAAGGTGGTGTCCATAATTTGCACTCCTATGAAAAACGTCTATACAATTGAGTAAGCATCCATAGATATTTAAAAGTTTATTTTTGCATATAAATATACCTTCATAGAGATCAACAAAACTAAAATAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTATCTGTTATTATTTGATGCTTTAACCAAAGGATATTGGACCAAGTCAAT
+
!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFF,:,,,,::,,,,F,:,FF,::,F:,:::,::F,,,,:FF,,,F,F:,,F,FF
Processing time:                0.005 seconds.

Input:                          2 reads                 499 bases.
Contaminants:                   1 reads (50.00%)        249 bases (49.90%)
Total Removed:                  1 reads (50.00%)        249 bases (49.90%)
Result:                         1 reads (50.00%)        250 bases (50.10%)

Time:                           0.025 seconds.
Reads Processed:           2    0.08k reads/sec
Bases Processed:         499    0.02m bases/sec

[kinase]

Oh boy, that's a dumb mistake on my part. Thank you for pointing that out.