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Hi,
I just tried to install changeseq following the procedure described in the README using git clone, not conda) and have experienced a couple of issues:
1. `biopython==1.76` and `pandas` seem t…
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1. It's not clear what Gene Resource data to download from BioMart. I'm using the built in Hg38 gene info as a template but BioMart doesn't have "NCBI gene ID" or "Transcript support level (TSL)" avai…
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### BioProject Checklist:
---------------
- [ ] PRJNA526626
- [ ] PRJNA567655
Follow the [Gene Expression Protocols](https://github.com/mestato/statonlabprivate/wiki/Gene-Expression-Analysis-Las…
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I encountered an error in GDCprepare.
There are the codes:
`query.exp Add clinical information to samples
Error in xj[i] : invalid subscript type 'list'
`
Thanks.
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Dear Alex,
Would it be possible to include in the next iteration of the manual, a visualization of how STAR counts reads with regards to read position with respect to one or multiple (overlapping)…
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Hi,
I wonder if anyone in this community can help me figure out the reason behind the discrepancy in counts. Please see below:
I am using HTSeq-count to generate counts from two different types …
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- [ ] logging
- [ ] automated indexing for `genome` table?
- [x] change index function
- [x] use `flock` to prevent multiple `cwl_creater.py` run
- [x] a workflow parser to generate graph
- [x] m…
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I've been trying to match up TCGA barcodes to filenames, and am struggling to do this with the new GDC system. I came across this issue ( https://github.com/NCI-GDC/gdc-client/issues/79 ), and was ho…
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CoverageBed counts more reads overlapping with peaks than the number of peaks overlapping reported by clippers internal count.
I'll Investigate this
@mlovci is there something with the read counting …
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Can I use this tool on local bam files for my project? I haven't submitted my data to SRA yet!
**python counter.py --inp test/Test1.bam --out Test1_counts --gtf test/ref-transcripts.gtf**
Error:…