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Hello,
I have made pggb graph for a gene and I am trying to run `vg rna` using:
```
vg convert -g smooth.gfa -p > example.pg
vg index example.pg -x example.xg
vg snarls example.xg > example.sna…
GSgen updated
2 years ago
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RefSeq transcript sequences can be different from the reference sequence (even if they agree with 1 build they can be different across builds). These sequences are aligned against the genome to produc…
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Context: I have paired-end RNA-seq data from a stranded library preparation protocol. I would like to identify differential splicing events between two groups (including cryptic exons). Is it possible…
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Hi, thanks for the great package.
I got the following block:
```
#+begin_src python :tangle /ssh:g5:/mnt/e/epi25/WES/migren/get_intervar_and_format_table.py
import pandas as pd
pairs = {
"a": …
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Hi, I am not able to get the annotateCTSS() working properly using my gff3 file.
I have tried both using Genomic Features (TxDb) and rtracklayer
```
> Hv_Morex.pgsb.Jul2020.HC_txdb HCgenes ce HC…
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Hi Jack,
In the output tabular file, the lengths don't appear to be correct? Using the large input dataset, the length for the first transcript (TCONS_00000024) is shown to be 966, when it should act…
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one locus match two different transcripts of the same gene, how to interpret this?
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Hi @chrishendra93,
I'm trying to reproduce part of Fig. 2d and 2e using the HCT116 and VIRC models provided in Git to verify that my installation of m6anet is intact and that I can run it as intend…
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Hi Matthias,
Thank you for making such a nice tool!
I would be interested to use it but I cannot seem to format my gff so that it would be compatible.
What version of tabix should I be using?
I'…
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Hello,
while testing this tool I ran into two issues. For the first one I can make a pull request and I can add the fix for the latter problem too, but for that I am unsure what behaviour is desired.…