Master bug for paired-end 3′ digital gene expression assays

[SuhasSrinivasan]

Description of the bug

Dear Developers,

Thank you for reviewing the reported issues.

This issue notes all the parameter changes needed for the issues reported in #1543 and #1544.

When using paired-end sequencing with Lexogen QuantSeq 3‘ mRNA-Seq FWD, the Custom STAR parameters in the docs need an update.

--extra_star_args "--clip3pAdapterSeq AAAAAAAA AAAAAAAA --clip3pAdapterMMp 0 0"

Possible values for clip3pAdapterMMp are 0, 1 and 2.

Final custom STAR parameters

--extra_star_align_args "--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMultimapNmax 20 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA AAAAAAAA --clip3pAdapterMMp 0 0"

Command used and terminal output

--extra_star_align_args "--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMultimapNmax 20 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA"

Relevant files

No response

System information

Version of nf-core/rnaseq: 3.18.0
Nextflow version: v24.10.5
Container engine: singularity-ce version 4.1.2-jammy
OS: Ubuntu 22.04.5 LTS x86_64
Executor: Local
Hardware: Desktop

[pinin4fjords]

We already have the other two issues, let's not multiply further.