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Hi Zhenxing,
I split the positive strand into a.fwd.bam, then I use a.fwd.bam to call m6A motif. I get 109757 peaks totally, and about 20% of them are located in the negative strand. In addition, t…
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Dear developers:
Hello and recently I was using VG to make a variant graph of a plant species and I want to compare the number of reads of one accession mapped onto the graph-based genome via vg gi…
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Hi there, I'm trying to run doctor.py to check the installation
~/bin/doctor.py
I get this message:
$ ~/bin/doctor.py
# Doctor! Doctor! Give me the news.
# Checking symptoms ...
# bwa …
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# command
geneBody_coverage.py -r /xxx/mm10/mm10_RefSeq.bed -i xxx_cutadapt.bam -o geneBody_coverage_output
# log
@ 2022-08-22 00:58:30: Read BED file (reference gene model) ...
@ 2022-08-22 00:58…
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I'm having some issues with the calculateChromosomeRelativeCoverage function running with the tumor_cov object being addressed at a nonexistent index. What do you believe could cause this?
```
…
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Right now, only 1 thread per file is used. Compression easily has enough work for multiple threads and it would speed up the runtime
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Hi, I am having an issue when I try to run the align and estimate RSEM. The first weird thing is that even though I am specifying the output location and have binded my singularity run to the current …
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Somehow I'm ending up with a very low number of duplex reads after using Dorado duplex basecalling with the following command (used the ligation sequencing kit V14 SQK-LSK114):
`dorado duplex dna_r…
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We may need a new CWL hint to collect the version number
```
hints:
VersionQuery: [samtools, --version]
```
- [ ] Write SchemaSalad for this as an extension
- [ ] Implement in `cwltool`
-…
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Hi,
I wonder how to pass several bam files to provide evidence for gene prediction. I would like to avoid to use samtools merge not to create chimeras. I am running trinity first on each sample. I w…