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I specify the parameters of UMITools to construct the UMI from R1+R2 and then discard R2 (see below).
However, the trimmer (FASTP) afterwards reports that all reads are low quality or too short.
-[nf-core/rnaseq] Pipeline completed successfully with skipped sampl(es)-
-[nf-core/rnaseq] Please check MultiQC report: 18/18 samples skipped since they failed 10000 trimmed read threshold.-
I believe that this is because FASTP is called with both R1 and R2, instead of discarding R2 (see full log file below), which produces empty .fastp.fastq.gz files:
Description of the bug
I'm trying to process bulk Smart3-seq data using the pipeline (related Slack discussion here). In my case, the FASTQ read structure is the following:
I specify the parameters of UMITools to construct the UMI from R1+R2 and then discard R2 (see below).
However, the trimmer (FASTP) afterwards reports that all reads are low quality or too short.
I believe that this is because FASTP is called with both R1 and R2, instead of discarding R2 (see full log file below), which produces empty
.fastp.fastq.gz
files:# all reads removed fastp --in1 FF230228_13_1.fastq.gz --in2 FF230228_13_2.fastq.gz --out1 FF230228_13_1.fastp.fastq.gz --out2 FF230228_13_2.fastp.fastq.gz
The reason for this is that if I manually run FASTP on R1 only, it will preserve a non-zero number of reads:
# retains most reads fastp --in1 FF230228_13_1.fastq.gz --out1 FF230228_13_1.fastp.fastq.gz
A similar issue was fixed by exposing the
--umi_discard_read
parameter, but I guess FASTP trimming was not included: #750.Workaround: Not using FASTP but TrimGalore (the default) also processes the samples correctly (and outputs only one FASTQ per sample after trimming).
Command used and terminal output
Relevant files
FF230228_13.fastp.log
nextflow.log
System information
Nextflow = 22.10.1
Ubuntu Linux = 20.04.6 LTS
nf-core/rnaseq = 3.11.0
local executor
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