Split interleaved output
Poshi opened this issue · 0 comments
Poshi commented
I'm trying to get a splitted interleaved output for a pair end experiment, but I cannot find the proper command line. Is this even possible?
I tried
$ fastp --in1 input_1.fastq.gz --in2 input_2.fastq.gz --stdout --split 2
ERROR: splitting mode cannot work with stdout mode
and
$ fastp --in1 input_1.fastq.gz --in2 input_2.fastq.gz --split 2 --out1 /tmp/test.fastq
ERROR: paired-end input, read1 output should be specified together with read2 output (--out2 needed)
But no luck so far.
I also tried interleaving first and splitting later, but it doesn't work either:
$ fastp --in1 input_1.fastq.gz --in2 input_2.fastq.gz --stdout > /tmp/test.fastq
.
.
.
$ fastp --in1 /tmp/test.fastq --interleaved_in --out1 /tmp/test.split.fastq --split 2
ERROR: paired-end input, read1 output should be specified together with read2 output (--out2 needed)
I could also try to perform the split in the first place and then iterate over the several files to interleave them, but this is quite cumbersome.