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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/169) by Irantzu A (Bitbucket: [iraun](https://bitbucket.org/iraun), ).**
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Is it possible to …
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# To Do
- [x] Literature review of spliced short read alignment methods (is anyone using Minimap2?)
- [x] Review Rust libraries for alignment and minimizers
- [x] Make stand-alone command line Ru…
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similar to this issue #422 , but I still have that after upgrading to 3.6.0.
```
> assays(oldse1)$count[grepl('BambuTx', rownames(assays(oldse1)$count)),] %>% rowSums() %>% sort %>% head
BambuTx5…
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Hi,
I'm interested in quatifying the PSI of a 5' splice site in a particular gene. The event is not in my annotation, but I can see that it's used in my bam files (on IGV). So I've decided to use t…
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## Need
### TMB calculation today in BALSAMIC
The current definition is based on:
1. TMB was defined as the number of somatic, coding, base substitution, and indel mutations per megabase of genome …
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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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## Data Subsetting to an even smaller size
Preparing Environment
```
conda activate ngs1
conda install seqtk
```
Subset small number ; For test only;
`for file in ./*.fastq.gz ; do echo $…
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Hello!
I noticed that introns less than 50 bp in length are apparently not recognized by IRFinder. I'm currently working with very small introns, between 31 and 44 bp, is there any way I could use …
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Dear Yuanhua,
This is more a question than an issue. I recognized that the counts in the fractions.tsv file can adopt non integer values, because the counts are the mean of Cnt_all .
Cnt_all is…
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Hi there! I read in this previous issue, that you guys were working on developing a version of rMATS to work with ONT data (https://github.com/Xinglab/rmats-turbo/issues/8) .....Has there been any upd…