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In the current setup, all genes with
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hey! thanks for developing this fantastic tool! I've been using it with great results and included it in a number of pipelines, with plans to include it the the `nf-core/riboseq` pipeline as a P-site …
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Hi Roleren,
Thank you for such a great and powerful tool like ORFik. It's excellent and well-written or explained.
Although, I have a few questions about the manual and my results:
1. In the OR…
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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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So I'm trying to run clear_quant on a RNA-seq file I obtained online (Ribo-), but I cannot seem to move past the following error:
> ###Parameters:
> Namespace(bowtie1='/home/nilu/Alignment_db/base…
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Hi,
I am mapping my Ribo-seq data, which are very short(about 30nt), to my reference. Here is my command:
```
STAR --runMode alignReads \
--runThreadN $t \
--genomeDir ${mhSTARindex} \
--re…
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Hi developers,
I'm assembling an eukaryotic genome with SPAdes 3.13.1 and ran into err code: -11 after K21:
```
0:43:49.631 26G / 35G INFO K-mer Index Building (kmer_index_builder.hp…
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I have been trying to use scikit-ribo on mouse ESC Ribo-Seq data but the output files generated from scikit-ribo-build do no correctly parse the given input GFF file. I am using the mm10_knownGene GFF…
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Hi, is it a desired behavior? Size of resulting data.table is very similar if you keep names as factor.
library(ORFik)
attach(loadNamespace(ORFik)
##only change is the if statement for keep.nam…
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Hi Saket,
Thanks for developing this great tool! I am surprised to get these results for the `psite_offsets.txt`output file:
```
relative lag to base: 33
lag of 28: 0
lag of 22: 0
lag of …