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Master bug for paired-end 3′ digital gene expression assays #1545

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SuhasSrinivasan opened this issue Apr 23, 2025 · 1 comment
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@SuhasSrinivasan
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SuhasSrinivasan commented Apr 23, 2025

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

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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

@SuhasSrinivasan SuhasSrinivasan added the bug Something isn't working label Apr 23, 2025
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We already have the other two issues, let's not multiply further.

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