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Hello,
Thank you for developing this nice tool.
I'm interested in analyzing allele-specific expression (ASE) in my single-cell RNA-sequencing (scRNA-seq) data. This data comes from offspring tissues…
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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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We are using Salmon to help allocate multimapped reads in dual RNA-seq data. What this means is we combine a host and pathogen genome (bacterial genome + host transcriptome) and also use a combined an…
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When I used the example data to test the program, I get an error
```bash
Error in file(con, "r") : cannot open the connection
Calls: readLines -> file
In addition: Warning message:
In file(con, "…
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### Description of feature
By default, Salmon will drop transcripts with identical sequence, as described here: https://github.com/COMBINE-lab/salmon/issues/214#issuecomment-381580235
This behav…
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Hi!
I've already read the other issues about this topic but I still have some question regarding duplicate transcripts.
If already exists an issue about the same problem I have, I'm sorry but I didn…
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Would be great if we can list the software or bioinformatic pipelines required for de novo RNAseq analysis.
Pipeline to add:
- [x] FastQC
- [x] MultiQC
- [x] [Trimmomatic](https://bioconda.git…
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I would like to use KMA, but I use HISAT2 and cufflinks for the alignment and quantification. How can I implement KMA in this pipeline for intron retention detection?
Thanks in advance!
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hi, Dr. Zhang,
I'm running the Darts_DNN, and I have several questions to ask. I have run Darts_BHT, and I have learned Darts_DNN get_data, and Darts_DNN build_feature, now I'am confused with Darts_D…
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Hi,
This is not an issue, but I'm just looking advice on this problem I've been trying (with limited success) to tackle on my own for a while.
First, I've been using salmon for years and I love …