Hi all Great to be a part of this community Just started usi nf-core #rnaseq

Hi all! Great to be a part of this community. Just...

Roumiana Alexandrova

04/09/2026, 2:36 AM

Hi all! Great to be a part of this community. Just started using nf-core/rnaseq - awesome tool with so many options, thank you to all the developers!

Jonathan Manning

04/09/2026, 8:20 AM

Thanks for the detailed investigation, and welcome to the community! You're correct - the discrepancy is because RSeQC

bam_stat.py

applies a default MAPQ >= 30 filter before counting, so its "Proper Pairs" figure only reflects high-confidence uniquely-mapped reads, while

samtools stats

counts all properly-paired reads regardless of MAPQ. The similar column names in the General Statistics table make this confusing. I've opened a PR to clarify the column labels: the RSeQC column will now read "RSeQC: Proper Pairs (MAPQ>=30)" and the samtools column "Samtools: Proper Pairs", with updated descriptions. See https://github.com/nf-core/rnaseq/pull/1776 Thanks for flagging this!

Jonathan Manning

04/09/2026, 9:58 AM

Update on this - we've decided this is best fixed upstream in MultiQC rather than in the pipeline config. As an immediate workaround, you can create a small YAML file (e.g.,

clarify_proper_pairs.yml

) with this content:

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custom_table_header_config:
  general_stats_table:
    proper_pairs_percent:
      title: "% Proper Pairs (MAPQ>=30)"
      description: "% Reads mapped in proper pairs with MAPQ >= 30 (RSeQC bam_stat)"

Then pass it to the pipeline:

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--multiqc_config clarify_proper_pairs.yml

This renames the RSeQC column in the General Statistics table so the MAPQ filtering is visible at a glance. We've raised this as an upstream fix in MultiQC itself (https://github.com/MultiQC/MultiQC/pull/3526) so future releases will have clearer labels out of the box.

Roumiana Alexandrova

04/09/2026, 2:35 PM

Thanks a lot for your quick reply, Jonathan!

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