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Instead of indexing the transcriptome at the start of each code block, I have indexed a copy of mm10 on AFW. Can this be changed in the code?
i.e.
rule quant_salmon:
input:
R1 = con…
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Dear salmon team and @k3yavi,
I am an happy user of alevin on scRNAseq data (10x). In some circumstances, I have to compare samples from very uneven sequencing depth (less than 100k reads per cell …
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Sample-specific sorted BAM files can be found in each sample-specific subdirectory here:
https://gannet.fish.washington.edu/Atumefaciens/20210726_cvir_stringtie_GCF_002022765.2_isoforms/
There's…
kubu4 updated
2 years ago
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I created RSEM index based on the eastern oyster genome gtf file where I only considered transcripts based on the GNOMON source (this only appears to
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Hi,
I used the new version of Aeron, but when I run the step of "rule fusionfinder" in the Snakefile_fusion, there always have the error.
The log file is :
Fusion finder Branch develop commit f9a…
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STAR already provides an awesome function for generating a transcriptome alignment for downstream tools such as RSEM, Salmon via `--quantMode TranscriptomeSAM`. As far as I understand, the alignment i…
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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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We have a two sets `[A x B]` and `[C x D]` of F0 animals which were short read sequenced. The F0 ([A x B] and [C x D] )were repeatedly mated to give `F1` `[AB]` and `[CD]`. The F1 were then mated to…
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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…
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
bulk mode
**Describe the bug**
```
Version Info: This is the most recent version of salmon.
### salmon (sele…