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**Describe the issue**
I am executing this command as per 'box 2' in Nat. Biot. 2024 article:
~$ kb ref -i fpa_index.idx -g fpa_t2g.txt -f1 fpa_cdna.fasta cds_from_genomic.fasta genomic.gtf
**W…
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The traceback:
```
Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
FileNotFoundError: [Errno 2] No such file or directory: '/home/rstudio/workspace//data/SspArc0008_10x_c…
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Hi,
I am trying to use BRIE using a custom annotation file and the GENCODE M10 annotation file. In both cases, running `brie-event` as follows:
`brie-event -a gencode.vM10.annotation.gtf`
ret…
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Part of GATK
> SplitNCigarReads developed specially for RNAseq, which splits reads into exon segments (getting rid of Ns but maintaining grouping information) and hard-clip any sequences overhanging …
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* spladder version: 3.0.3
* Python version: 3.9.12
* Operating System: Ubuntu 20
### Description
I am trying to run SplAdder on 83 samples using the instructions for Use on large cohorts ( htt…
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Hi Geo,
In my BAM file, there is a certain number of spliced read alignments which do not have the XS tag. My understanding is StringTie will ignore those spliced read alignments which do not hav…
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Hello rpvg team
I have a general question and I would appreciate your help.
I am trying to infer the haplotype expression of human-experiment reads using rpvg.
I have performed the construction o…
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Hi,
I am currently trying to run Taiji on a set of WT and KO RNAseq and ATACseq data. To not mess with previous analyses I decided to use the already existing gene quantification, which I did with …
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We're adding a new quantification challenge relative expression output. However, since the quantification challenge originally outputs TPM values, the ground truth data was also in TPM. Hence, we need…
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Hello,
Thanks so much for developing this tool, I find it quite easy to use.
I'm wondering what's causing duplicated transcripts (identical coordinates, different transcript id) to have differen…