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Hi, I intend to use the Riboflow pipeline for my new riboseq data from Rat. Previously I used Riboviz for my analysis. I am interested in using the new Nextflow pipeline. Can you add the rat genome re…
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The demultiplex pipeline currently takes a single annotation sheet, which is fine for almost all cases. Flow lanes can have multiple annotation sheets, where there is a mix of, say, CLIP and RNA-Seq s…
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### Setup
I am reporting a problem with Biopython 1.81, Python 3.10.9, and windows11 as follows:
```python
import sys; print(sys.version)
import platform; print(platform.python_implementation(…
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Hi!
Thanks for making this very versatile package.
I'm currently doing an analysis of bacterial ribosome footprinting data. I followed the steps in the different vignettes and everything mostly work…
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**Describe the bug**
The rrnaProbe command seems to do nothing, even with the correct file structure. Analysing the .py code reveals many inconsistencies with the documentation. Making the obvious ch…
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With the `c-elegans` test data, the `rpbp_predictions_dashboard` app does not execute. The reason is that it looks for an output file `WBcel235.chrI.fa.fai.txt`, where only `WBcel235.chrI.fa.txt` exis…
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I'm new to Riboseq, and, looking for helpful tools, have found this R package.
After reading the paper, I am still not sure, if it is the right one for us. We don't have RNA-Seq for our project, …
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Hi there,
I am trying to run ribotish on regular riboseq data from our lab.
Unfortunately, this already fails at the quality step. I mapped the reads to their reference (GRCm39) with a special ann…
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Dear ORFik team,
I am trying to use ORFik for analysing my Ribo-Seq experiments.
I create the experiment and everything seems to be working normal:
```
create.experiment(dir = dir,
…
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Hi,
I want to use your tool to analyze an E.coli dataset containing both classical RiboSEQ data and TIS data.
So far, I have been able to run all the modules independently as described in your d…