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### Description of feature
I'm noticing a lot of multi-mapping reads and those unmapped as 'too short'. Some of this is just down to the short read lengths I guess, but we should try to add some ST…
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### Description of feature
Here I attempt to break down the required/desired modules for each processing stage of the workflow:
### Pre-Processing
- [X] Quality Control (FastQC)
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- [X] Cu…
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- [x] Misannotated genes (supp table 4a)
- [ ] alternative intron retention (supp table 4d)
- [x] 11 ‘dubious appeared to be translated (did we change these to coding?)
- [x] 3 dubious were tra…
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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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Hi Cyril,
Thanks for your work - codonDT has the potential to be quite useful for our work.
I have matched riboseq and rnaseq data. I've run a test sample with only the riboseq to completion. …
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Hello,
Thank you for such a great publication/tool. I am attempting to run the riboseq pipeline, and am encountering issues stemming from the check_annotation() function in the general_functions.sh…
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Hello,
I am using PRICE software, it is really a wonderful tool, I have used it to predict ORF of several samples and it works well. Unfortunately, now I encounters a problem when analyzed a sample. …
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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 developing this tool and your paper comparing methods. I have a question about applying this method outside of the differentially expressed genes context and would like to know if you se…
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- [ ] In search.html, change div class `col-md-9` to `col-md-12` .
- [ ] Add `style="margin-right: 5px"` to page navigation buttons of tables.
- [ ] In **About** page, **Search** button looks di…