PRINSEQ-plus-plus
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The option -noiupac removes good reads
Hey Adrian, I just noticed that using the option -noiupac seems to remove reads erroneously. Here is an example read that gets removed even though it is only ATCG:
@SRR5677815.19460357 19460357 length=150 ATTCCCCTGGAGGTCTGTGGCCCCTGTATTATGCATGAAAGGTGGGAGGGTGGCCTTGAAGCCTAGAAAGAAGCAAAATGTTTATTCCTTAAGAGACAAGCTTTGACCTGTCACGGTGGCTCATATCTGTAGTACCAGTGCTTTGGGAGG +SRR5677815.19460357 19460357 length=150 AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJAJJFJJJJJJJJJJJJJJJJJJJJJJJAJJ<F
The command I run is:
prinseq++ -fastq test.fa -out_format 1 -out_good test_out.fa -out_bad /dev/null -min_len 60 -min_qual_mean 20 ns_max_n 1 -derep -lc_entropy -trim_tail_left 5 -trim_tail_right 5 2>&1 > test.log