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hi there,
I have reads aligned by STAR (first genome then transcriptome) and therefore the seqname read in by the bamtolist method is only the chromosome which then is not found in the generated an…
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Hi,
Our RNA-Seq protocol results in fragments that align to only the opposite strand of the transcript, but the riboseq reads align to the forward strand. Your pipeline assumes stranded reads will a…
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Hello,
I am trying to run the xpresspipe riboseq but I am getting the same error, I believe it's from the fastp package for UMI:
TypeError: can only concatenate str (not "int") to str
I tri…
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I don't think I have permissions to create new branches. For now, I've placed all the things @FlicAnderson theoretically needs to recreate the issues I'm having https://rutgers.box.com/s/3d0se6r1g48tb…
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Hello,
I'm using CircCode, such a powerful tool, but I have problem, every files I used here are from your example.
When I run: python3 make_virtual_genomes.py -y config.yaml, the err is:
No. 1 l…
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There should probably be `resfilelist` instead of `resfile` on line [no. 2533 in `RiboseQC/R/riboseq_analysis.R`](https://github.com/ohlerlab/RiboseQC/blob/cbc33c48dfa681110ff454d517fbee5f05669aec/R/r…
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Hi
I just started working on riboseq data, and came across ribo-tish which seems really useful for QC-ing. I have aligned my reads using STAR as per the guidelines and using the gtf annotation file…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/jipingw/RiboDiPA
Confirm the following by editing…
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Dear Plastid Team,
I have been using plastid for about a week now. Everything runs fine, no errors. **Metagene profile looks representative of regular riboseq data.**
However, the .bed file that…
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Following up on #2
are there any recommendation for duplicate reads if UMIs are not available?
Should the duplicate reads be marked or removed?
Other than processing efficiency, is there any ot…