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fastp PE read output bug #92

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colindaven opened this issue Nov 22, 2022 · 0 comments
Open

fastp PE read output bug #92

colindaven opened this issue Nov 22, 2022 · 0 comments

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@colindaven
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colindaven commented Nov 22, 2022 •
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  • mm2 PE and SE deliver same output
  • PE reads not listed properly in BAM or samtools flagstat of BAM
  • R2 not passed to minimap2 aligner properly from trimming

@PG ID:minimap2 PN:minimap2 VN:2.21-r1071 CL:minimap2 -x sr -a --split-prefix /bla/tmp_sample3_R1.trm -t 16 /bla/metagenref/wochenende/2021_12_human_bact_arch_fungi_vir.fa /blabla/nf_wochenende/work/4a/ad46d170bc8d8f6bb46c0fe4ab2437/tmp_sample3_R1.trm.fastq

Edit:
This was due to reads trimmed by fastp (PE reads) not being output correctly.

Workaround before bugfix:
use the standard trimmer trimmomatic
@colindaven colindaven changed the title minimap2short PE reads not read in properly fastp PE read output bug Nov 22, 2022
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