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At the moment, it's not clear what exactly the "Standard format" entails. Only once you try to use it and it errors out, you get info about what columns are actually needed.
Currently the docs jus…
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I have human RNA-Seq dataset it has two different barcodes in the different folder. I aligned with that command
minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam
I try to quantify and coun…
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Hi,
I am using StringTie (v2.0.3) to search for novel lncRNA transcripts. After running stringtie on my on individual samples, I use --merge to merge samples into a single gtf (with the ensembl ann…
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## Problem description
Some of my exons did not have a matching CDS. So I run the gt cds command to make sure that every exon had a CDS.
I got this message after it run for a few lines:
Asserti…
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We were running into errors I don't understand that were fixed with pymongo 3.1. Here's the traceback:
```
Traceback (most recent call last):
File "manage.py", line 58, in
manager.run()
Fil…
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We moved to rankscore, but raw scores are used in ACMGv4 in PP3_supporting
Check out if any others are used
We should also run eg REVEL as a tool instead of dbNSFP
If not on the short variants then…
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### Affected tool(s)
ConvertToRefFlat
### Affected version(s)
- [X] Latest public release version [2.5.1]
- [ ] Latest development/master branch as of [date of test?]
### Description
I am a…
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### Description
Seems that Outrigger needs .chromInfo file but can't find it
There is also a conflit from Ensembl vs UCSC chr naming convention
### Steps to Reproduce
1. Alignwith STAR (OK) us…
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First of all, let me say thank you for sharing the great project!
But I'm having a hard time importing a new genome.
I found my gff needs to be modified before the import.
So I added some lines i…
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@iskandr is changing a few things around. Also, his comment from before:
> My only suggestion would be to maybe increase the minimum MAPQ to 1 and if you're ultimately using the counts of neoepitopes…