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Hi,
it seems that --writeUnmappedNames option doesn't work for `salmon alevin` (both R1 and R2 reads were used), while `salmon quant` with the same dataset (only R2 reads were used since R1 contains …
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Hi,
Currently the default output of `salmon alevin` is sparsed Matrix, but fishpond can deal only with regular matrix. E.g. trying to apply of `scaleInfReps` (v. 1.3.10) to `salmon alevin` (v.1.1.0) …
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I wanted to compare 3 PBMC and 3 Stimulated samples of scRNA-Seq run. I was wondering what would be the best way to process the data:
1) Process each of 3 PBMC separately using `CellRanger count` a…
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Thanks a ton for snakemake, it's great and intuitive!
I think it's related to #432 but I've made a minimal reproducible example to help.
Note that I've initially opened a question on [Stack Ov…
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Hi,
After my data preprocessing, I have a custom fastQ R1 composed just with the BC and the UMI.
My BC has length 18nt and the UMI has length 8nt. So the sequence in R1 has total length 26nt.
…
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Hello,
I followed: https://combine-lab.github.io/alevin-tutorial/2018/output-format/
`Pandas Compatibility`
I want the `csv` file of `alevin_df.`
Thank you in advance for great help!
…
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Alevin returns a `whitelist.txt` file - add option to import only barcodes listed therein.
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This would be super useful if you could pull it off... My sense would be that one could add an annotation in the bam tags and then quantify at the end of the computation...
http://velocyto.org/
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I quantified my samples using Alevin version 0.14.1 using the following command:
`salmon alevin -p 48 --tgMap transcript_to_gene.tsv -i ../Transcriptome/index -l ISR --chromium -1 Reads/SAMPLE_1.fa…
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Hi
I am using salmon 1.2.0 to build a Salmon-SAF index on Rat data from Ensembl -- using full genome as decoy.
```
wget ftp://ftp.ensembl.org/pub/release-96/fasta/rattus_norvegicus/cdna/Rattus_…