-
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…
-
Hi, I am using the pipeline for riboseq analysis and other than a couple of slight changes (just some salmon commands), it is working fine until the riboprof section, where this error is being display…
-
When having a:
exp_group = hdf[f'transcript/riboseq/{experiment}/5']
and succesfully extraced the ribosome matrix each of the matrices has the shape (tr_len*21).
As described the different ro…
-
```
What steps will reproduce the problem?
1.-bash-4.1$ ngs.plot.r -G hg19 -R genebody -C
/srv/gsfs0/projects/cho/riboseq/bam/R10_Rluc_control_arsenite_R1.hg19.bam -O
R10.genebody
.
What is the exp…
-
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…
-
As per the meeting on Oct 14, sometimes, a situation arises where there are reads in a file that you don't want to run through riboviz, for example, if you place RNAseq and riboseq reads together or s…
-
```
What steps will reproduce the problem?
1.-bash-4.1$ ngs.plot.r -G hg19 -R genebody -C
/srv/gsfs0/projects/cho/riboseq/bam/R10_Rluc_control_arsenite_R1.hg19.bam -O
R10.genebody
.
What is the exp…
-
While looking through the output & code of riboseqc, I've noticed that the determination of read_lengths is based only on the mapped part of each read, while soft-clipped parts of the read are ignored…
-
**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…
-
### Description of feature
sortmerna is implemented in the pipeline and runs by default. There will also be a bunch of other short RNA species we should remove, which we can use the (also inherited) …