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**tl;dr**: 3-tag sequencing methods for bulk RNA samples contain known sample indices and UMIs and thus resembles sc-RNA-seq read formats. Do you have a recommendation on how to use Salmon and / or Al…
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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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Hello,
I am currently following the `kallisto | bustools` tutorial on processing nuclear RNA-seq, which runs `bustools count` on spliced and unspliced transcripts. I know that you can specify `--g…
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The README states multiple BAM files can be provided to `bambu()`. Reading the entire documentation suggests the intention here is that each BAM corresponds to a separate sample to be analysed jointly…
cjw85 updated
2 months ago
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I did trinity assembly and then polished it using TransDecoder and cd-hit. Then I run the downstream analysis using `align_and_estimate_abundance.pl`, but got the following error:
```
Mapping Info…
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Hi,
Thank you for the tool. I am using it for isoform quantification. As a test run I am testing it on one sample from 10xV2.
The command that I am using
`scasa --fastq ERX3806131/4861STDY74…
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Hello ITMAT Bioinformatics Laboratory team,
I have been trying to use CAMPAREE to generate transcripts from an RNA sample. I would like the resulting transcripts to be equal to the reference genome…
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Dear samtools developers,
This is Bo Li, the developer of RSEM. When I used samtools sort -n to make sure the alignments are grouped by read names, I found an issue. If we have paired-end reads, samt…
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When aligning RNA-Seq reads simulated from transcripts extracted from genome+annotation, many (unsurprisingly) align to an incorrect splice-form. Basic, rnf-style evaluation focuses on the exact posit…
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Christos Efthymiopoulos, Rocio Isabel Paez
> Starting with Arnold's pioneering work, the term "Arnold diffusion" has been used to describe the slow diffusion taking place in the space of the action…