Running prinseq-lite with both files of paired-end reads, I obtained the kind of result.
All sequences had the same size after trimming (only five bases at 3' and 5' positions)
But, doing the same with the files, one by one, the results were as I expected only trimming. I mean, the forward trimmed sequences had the same number of sequences than the reverse. Does anyone had this problem?
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-rw-rw-r-- 1 301M nov filtered-19A_test.good_2_singletons.fastq
-rw-rw-r-- 1 301M nov filtered-19A_test.good_2.fastq
-rw-rw-r-- 1 301M nov filtered-19A_test.good_1.fastq
-rw-rw-r-- 1 299M nov filtered-19A_test.good_1_singletons.fastq