I want a option for keeping or discarding PE read with poly-A/T in R1/R2 after using "--poly-a" option,
but "--trimmed-only" or "--discard-untrimmed" option is only work for adapter trimming
Example of "--trimmed-only" and "--poly-a" as below:
cutadapt --trimmed-only --poly-a --pair-filter=any test_1P.fq test_2P.fq -o test_1P.trim.fq -p test_2P.trim.fq
This is cutadapt 4.5 with Python 3.9.6
Command line parameters: --trimmed-only --poly-a --pair-filter=any test_1P.fq test_2P.fq -o test_1P.trim.fq -p test_2P.trim.fq
Processing paired-end reads on 1 core ...
Done 00:00:00 10 reads @ 949.2 µs/read; 0.06 M reads/minute
Finished in 0.023 s (2337.050 µs/read; 0.03 M reads/minute).
=== Summary ===
Total read pairs processed: 10
== Read fate breakdown ==
Pairs discarded as untrimmed: 10 (100.0%)
Pairs written (passing filters): 0 (0.0%)
Total basepairs processed: 2,174 bp
Read 1: 1,351 bp
Read 2: 823 bp
Poly-A-trimmed: 242 bp (11.1%)
Read 1: 54 bp
Read 2: 188 bp
Total written (filtered): 0 bp (0.0%)
Read 1: 0 bp
Read 2: 0 bp
=== R1 poly-A trimmed ===
length count
0 8
21 1
33 1
=== R2 poly-A trimmed ===
length count
0 7
20 1
46 1
122 1
I want a option for keeping or discarding PE read with poly-A/T in R1/R2 after using "--poly-a" option, but "--trimmed-only" or "--discard-untrimmed" option is only work for adapter trimming
Example of "--trimmed-only" and "--poly-a" as below: