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Hi,
I would like to use RSEM to quantify some nuclei RNA-seq data.
STAR version=2.7.9a
RSEM version=1.3.3
The code I used are:
###generate rsem reference
#use GRCm38_102 genome and gtf …
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### Description of feature
Specifying parameters via `-c custom.config` can make problems with DSL2 workflows. The corresponding documentation was added in https://github.com/nf-core/tools/pull/217…
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Hello ITMAT Bioinformatics Laboratory team,
I have been trying to use CAMPAREE to generate transcripts from an RNA sample. I would like the resulting transcripts to be equal to the reference genome…
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We currently have a function in oncopipe ([generate_pairs](https://lcr-modules.readthedocs.io/en/latest/oncopipe/oncopipe.html#oncopipe.generate_pairs)) that handles the complex task of matching up tu…
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### Description of the bug
not sure how to handle technical replicates in contrast file? i have a samples.csv like one presented at https://nf-co.re/differentialabundance/1.4.0/docs/usage but with on…
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Hello,
Firstly I would like to thank you for this amazing tool.
I've dealt with aberrant splicing analysis using DROP workflow for 203 samples. During the analysis the execution was corrupted, and…
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Hey, @jelmerp! Sorry for being a bit late. I was thrown off by having to create a new repository due to issues with pushing to the last one.
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Hi,
I am currently trying to run Taiji on a set of WT and KO RNAseq and ATACseq data. To not mess with previous analyses I decided to use the already existing gene quantification, which I did with …
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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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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