-
`/Users/jonatan/Micropeptide_project/psiclass/junc /Users/jonatan/Micropeptide_project/EGAF00001593233.sorted.bam -a > ./splice/psiclass_bam_0.raw_splice
/Users/jonatan/Micropeptide_project/psiclas…
-
I split vcf, fasta and gtf according to chr, and followed the steps of [https://github.com/jonassibbesen/vgrna-project-paper/tree/main/scripts/bash/contruct_pantranscriptome](https://github.com/jonass…
-
Hello to all
I was wondering if it would be possible for you to help me please. I have installed PASA but I am getting an error on execution. I have collected the error in the attached pdf, see if…
-
Idea: find a few examples of homology RRIs in human and mouse training data. Homologe x of the mouse can be then tested if it will be correctly predicted by the 'human model' and vice versa.
TODO…
-
I'm a new user of BRAKER, and overall I'm very impressed with the results, so great work!
I have a brief suggestion for a future update: I think the --addUTR feature could benefit from increased st…
-
### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
3.6.5 |Anaconda, Inc.| (default, Mar 29 2018, 18:21:58)
[GCC 7.2.0]
Lin…
-
Dear Brian.
We ran STAR-Fusion on a tumor sample.
The tumor sample was already known to contain a TMPRSS-ERG fusion, the fusion breakpoints could precisely be determined on the DNA level.
We a…
-
Hello,
Curious if the 5'prime partial ORFs, which lack start codon (M), should be considered for the downstream analyses?. Also, is it preferable to consider only the longest ORFs per gene/transcript…
-
Currently the app uses the `X` slot of the AnnData object for extracting expression values. It would be great to supports the `layers` slot and enable exploration of any assay (or matrix) from the Ann…
-
Hello,
I am currently using Salmon v1.2.0 which was build from source and is run on Ubuntu Linux
My objective is to obtain the proportions of different alternative spliced transcripts, which I …