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Hi,
I'm trying to count single end reads aligned to a genome with STAR, this command line i'm using:
`htseq-count -f bam ZF_C1F.Aligned.sortedByCoord.out.bam ../Annotation/ZebFish.ncbiRefSeqCura…
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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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- [ ] 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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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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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:…
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sorry for raising two successive issues with this R script.
i previously used the function to cache and return a SummarizedExperiment of HTSeq - Counts from TCGA data, and it worked fine without an…
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Each directory should include a module file that contains the name of the module used to create that directory. This information could be added to the SAMPLE_ID.versions file. The file containing the …
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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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Hi,
We would like to request a new feature that puts the result from multiple steps in a workflow into a new directory. This would help dramatically with file organisation in the final output direc…