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Dear Alex,
I am a new STAR user (this is the disclaimer for my putative dummy question). I am trying to align an RNAseq experiment to a Nicotiana benthamiana genome. **The GTF file does not contain…
ghost updated
4 years ago
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### Description of the bug
Hi,
I added this parameter to my pipeline --extra_star_align_args '--runThreadN 35', but it duplicates the parameter in star rather than replacing it. Here is the error I …
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cwlでつくる?
ymlでinput情報を揃える。
working dir等どうすればいい?
- https://github.com/Barski-lab/workflows/blob/master/tools/trimgalore.cwl
- https://github.com/common-workflow-language/workflows/tree/master/tool…
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Please List all the tools included in this repos by precedence ....
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### Description of the bug
I am running the most current version of @marchoeppner dev branch on Tower on a real dataset. The workflow passed repeat masking and produced the `consensi.fa` file but fai…
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Some tool choices in RNAseq are a matter preference, in that the evidence is not clear enough to enable an empirically or theoretically motivated choice. However, some things are just demonstrably bad…
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Hi,
I tried to use the rmats-4.1.2 version since I could not build the turbo version.
The installation seemed OK, but when I run the script below, it showed some errors.
Could you help with this? T…
circR updated
11 months ago
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### Description of the bug
After the recent update of the module [bea3ca9](https://github.com/nf-core/modules/commit/bea3ca998816a7f812b1bbbcb27c3a9ffbac0706), `ENSEMBLVEP` process fails:
```
-…
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Hi,
Even if I found multiple times the error, I can't figure out what's wrong. I got this bam mapped with RNASeq pipeline from Nextflow, and I want to get curve (from SMARTSeq in fact). However, I …
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Hello,
I am running into an issue trying to produce the Chimeric.out.Junction file for large files. I have a pipeline using STAR 2.7.7a with the command
```
STAR --genomeDir `pwd`/{params.inde…