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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.
The text was updated successfully, but these errors were encountered:
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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
and
But no luck so far.
I also tried interleaving first and splitting later, but it doesn't work either:
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.
The text was updated successfully, but these errors were encountered: