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The codes below are quoted from the notebook.
```
sos run splicing_calling.ipynb psichomics \
--cwd psichomics_output/ \
--samples sample_fastq_bam_list\
--splicing_annotation hg38_su…
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Enjoying the great tool, but I have another question:
One of my sample had following stats of used and unused reads (following the 2-pass alignment strategy with STAR)
read outcome totals across a…
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First and foremost, I would like to thank you for developing the fantastic DIA-NN tool.
I am currently working on a project where I aim to distinguish and quantify isoforms produced by alternative …
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I am using Salmon (Salmon 1.3 installed through homebrew on mac ventura 13.5.2) for quantification in alignment mode. I have bam files (aligned to transcriptome) for nanopore data from Minimap2, which…
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Hi,
Could you please clarify what if the difference between NA and missing values in the files named SE.MATS.JCEC.txt?
In other words, if I were to merge the SE.MATS.JCEC.txt file from multiple sa…
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Hi,
I am using the "samples.csv.gz" file generated by brie (splicing quantification) as a "miso_files" input for the sashimi plot. However, no posterior plot is generated. You showed in the 'https:…
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Hi,
I did not see any examples analyzing other splicing types (A5SS, A3SS, MXE, RI) using BRIE. I used brie-event-filter to deal with gff3 of other splicing types, but I can not get gold.gtf or gold.…
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Several present at the [Dec 2018 meeting](https://github.com/riboviz/bbsrc-nsf/blob/master/docs/minutes/20191203-Dec2019meeting.md), argued that genome-centric alignment is good for quality control an…
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For gene-body internal last exons currently the uniquely-exonic regions for each last exon are passed as regions for Salmon to quantify. e.g. for a bleedthrough event, the annotated internal exon is s…
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Hi Yuanhua,
I want to perform differential splicing of different groups of single cells. Could you provide an example for groups as I did not find this in the manual.
Thanks
ghost updated
2 years ago