-
According to https://github.com/COMBINE-lab/salmon/issues/434#issuecomment-540533728 the current behaviour of the Alevin wrapper in which each fastq file provided in a collection is analysed separatel…
pcm32 updated
4 years ago
-
Hi,
I have been having issues recovering the same amount of cell barcodes post correction in salmon alevin compared to cell ranger. Maybe alevin-fry can help in this task?
**What I have**
- scRNA…
-
Hi, thanks for your previous responses a while back.
I am now trying to use cellSNP/Vireo with a SAM/BAM output file from `salmon alevin` instead of Cell Ranger, and wanted to see if this would be …
-
Hi all
I have been working with the raw fastq files from [this study](https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA590042&o=acc_s%3Aa), and tried to map them using `Alevin`.
following `fa…
-
After making sure the Alevin project compiles to get the jar file, when I try to run CoordVNF main class, it throws an error saying it requires project called alevin-svn. I searched everywhere but cou…
-
I’m doing an analysis using salmon alevin command and after running the command the process stops at around 25% of analysed cells (that’s around 6500 cells - I know that from the output log). It happe…
-
Tutorial: https://www.kallistobus.tools/velocity_tutorial.html
The sticking point is getting introns programmatically from every possible GTF. I've had success with [gffutils.FeatureDB.create_intro…
-
## Description
Add support for `h5ad_alevin` in the api.
### Steps
1. Add the file type in `signedUrl.js`
2. Update request validation in `CreateSamples.v2.yaml`
-
Hi @AndreasHeger @jscaber I have been developing a single cell pipeline using bus tools and alevin (salmon) for dropseq methods : https://github.com/Acribbs/single-cell/tree/master/pipelines.
I was…
-
There has been a small amount of discussion about the BD Rhapsody barcode / sequence format (e.g. see [here](https://github.com/COMBINE-lab/salmon/issues/445#issuecomment-551083490)), but it would be …