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Hi,
Thank you for continuing to develop ORFik!
```
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS
ORFik_1.22.2
```
It was observed …
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Dear Dobin,
I'm using STAR to map the Ribo-seq results to a genome. I ran the program with and without the "--twopassMode Basic" parameter, and found that by using the 2-pass mode, the alignment ra…
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Thank you for your great package to analysis differential translation events on ribo-seq data. I am using your package to analysis my own data,but my rnaseq and riboseq data do not have replicates,how…
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Thank you for the great tool!
It seems to be working perfectly for me but I would like to request a feature implementation.
Would it be possible to add a column of in-frame Ribo-seq (not TI-seq) c…
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I have tried running both the run_ORQAS.sh script and running the pipeline step by step. I have tried using my ownrnaseq and riboseq data and the sample data. I keep getting the same error.
termin…
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Hi, when viewing the ribo-seq plots from the PausePred result table, ribo-seq coverage is set to True by default
Is this by intention or would it be possible not to be set to True by default?
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Hello,
I just used the _Ktrim_ to trim Ribo-seq reads, but i found it did not work. then, I tried _galore_trim_ and _galore_trim_ could trim residual adaptor from the reads.
```
`[ymwang @ ~/linqin…
Ci-TJ updated
3 years ago
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**Topic name:** ribosome profiling
**Short description:** With ribosome profiling, ribosome-protected mRNA fragments are analyzed with RNA-seq techniques leading to a genome-wide measurement of th…
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hey, testing the package on Alexaki et al 2019 (human Ribo-seq)
Got an error I think is a bug, because I use a sparse bam file (2 Million reads only):
```
./RiboNT --gtf /media/roler/S/data/Bio…
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**To Do:**
- [x] anndata warnings (https://github.com/samuel-marsh/scCustomize/issues/162)
- [x] LIGER 2.0 compatibility or warning messages (https://github.com/samuel-marsh/scCustomize/issues/161)
…