#CE6SDBX2A with #CE8SSJV3N error: I am getting the error (see attached screengrab) when I use GTF from NCBI. It like it was fixed in this issue : github.com/nf-core/rnaseq/pull/1889. but still come up when I run rnaseq 3.26.0 . Is there a way of getting around this problem?

Hi, @Javan Okendo! Slack uses channels to organise discussions. Press the

...

more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @Igor Trujnara for help.

The pull request you are referring to was closed and never merged. The NCBI GTFs don't have the

gene_biotype

field, so you cannot summarize the results by biotype in the MultiQC report. You have the following options: • Use a GTF with

gene_biotype

field. I am not a fan of NCBI GTFs, because they can have various issues (such as this one), and more importantly, there are no clear versions in NCBI, which affects reproducibility. I like Ensembl. • If there is another field of interest, you can summarize by that one -- use the

--featurecounts_group_type

parameter to specify which one. • If you need to use the NCBI GTF and are not interested in summarizing over another field, use the

--skip_biotype_qc

parameter. BTW, for questions specific to the rnaseq pipeline (such as this one), the best place to ask is the #CE8SSJV3N channel. (Also, Slack does not have "hashtags" like some social media, #CE8SSJV3N refers to the channel called

rnaseq

, and #CE6SDBX2A to the (this)

help

channel. This notation just allows for hyperlinks that take you to the respective channel, it does not do anything else.)