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nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
https://nf-co.re/rnaseq
MIT License
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Add support to use the pipeline with NGS generated using zymo research kit #1337

Open Ahmedalaraby20 opened 2 months ago

Ahmedalaraby20 commented 2 months ago

Description of feature

https://www.zymoresearch.de/products/zymo-seq-switchfree-3-mrna-library-kit

MatthiasZepper commented 2 months ago

I presume you can analyze the data already with the current pipeline version. After all, the parameter suggestions/UMI settings are just examples and not an exhaustive list. So if your favorite kit is not named, you could still make it work by choosing the pipeline parameters accordingly.

All the listed settings and recommendations in the docs have been worked out by users of the pipeline and kindly shared with everyone else.

I appreciate, that the complexity of the pipeline can be overwhelming, and we are happy to help, if you can't figure something out, but please make an own effort first. Instead of just opening an issue with the URL to the kit's manual for others to read it for you, please summarize the key characteristics of the kit and propose some parameter settings that seem appropriate to you. Then we are happy to chime in and double-check for your peace of mind. Thanks.

Ahmedalaraby20 commented 2 months ago

Thanks, a lot, I was not aware that this was going to open a ticket, I thought it was some sort of suggestion box, Anyway, you are totally correct, my fault sorry,

MatthiasZepper commented 2 months ago

No worries, I didn't take offense. Becoming familiar with git and GitHub takes a while for everyone, and it is great to see new members in the nf-core community. Welcome!

If you like, you can join the Slack workspace as well, which is our community's main discussion platform. Here, we have multiple dedicated channels for topics ranging from #rnaseq to starting as a contributor, and you can ask as many questions as needed. Since documentation updates are a great first pipeline contribution (see e.g. pull request #1314) it would be great if you could suggest something to help other users of that kit!