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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.
clip3pAdapterMMp
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"
--extra_star_align_args "--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMultimapNmax 20 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA"
No response
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
The text was updated successfully, but these errors were encountered:
We already have the other two issues, let's not multiply further.
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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.
Possible values for
clip3pAdapterMMp
are 0, 1 and 2.Final custom STAR parameters
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
The text was updated successfully, but these errors were encountered: