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Hi,
I tried to run TRUST4 on paired end Bulk RNA-Seq Fastq files, but it failed with "139 at ./run-trust4 line 54" as shown in the screenshot below. Could you tell me what this error message means a…
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- [ ] Have a quick start vignette showing some content similar to https://bioconductor.org/packages/release/bioc/vignettes/recount/inst/doc/recount-quickstart.html#2_Quick_start_to_using_to_recount ht…
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First of all thank you for this nice tool.
I run nebula for differential expression analysis between 2 groups and I realised that my top (by logFC) significant genes are mostly driven by some outlie…
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Dear @czarnewski
Thanks for your beautiful paper and code!
I want to use scRNA-seq data with cell type annotation to deconvolution my bulk RNA-seq.
But I only find scRNA-seq raw data and cod…
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Hi @alexdobin
Thanks again for writing & maintaining STAR. The latest diploid mapping feature is very cool. I was wondering how difficult you think it would be to extend it even further, to map to …
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Hello @masai1116,
Thank you again for sharing the code! I have some questions regarding RNA-seq reads.
In our test SHARE-seq data, if we filter R2 by polyT, `TTTTTT + 1 mismatch`, about 50% rea…
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Hello,
I am currently following the `kallisto | bustools` tutorial on processing nuclear RNA-seq, which runs `bustools count` on spliced and unspliced transcripts. I know that you can specify `--g…
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I wonder why avg_LFC column is multiplyed by "-1" in libra pseudobulk RNA seq output file.
I think It changed the direction of expression in DEG genes.
For example ,I ran the pseudo bulk RNA seq …
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Hey,
I have a question: my matrix in the "calculate_reaction_score", considering bulk RNA data, must be normalized? In which way? TMM, TMP,log2? I don't see any directive.
Thank you
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Hi
I am using raw count data from single cell RNA-seq and bulk RNA-seq.
I am currently stuck at running the deconvolution function solveDampenedWLS().
I get the error :
```
Error in solve…