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I'm aligning long assembled contigs (from Supernova) to hg19. Occasionally bwa mem will generate long runs of bad alignments with many long indels, for sequence that actually matches well.
From tra…
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`chr8 77023607 Minda_142 N . PASS SVLEN=16825;SVTYPE=DEL;SUPP_VEC=ILL_MantaDEL:146943:2:3:0:2:0,ILL_3569376030:2,ILL_gridss146fb_20854h,ONT_severus_DEL8304
`
https://v2.genomeribbon.com/?session=htt…
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I have a set of high-confidence consensus SVs called from illumina WGS data which I want to compare to SVs called with nanopore long-reads. There seems to be a surprisingly large number of variants wh…
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There is several tutorials that would need some ❤️
Most of the changes are newcomer-friendly 😄
We created a checklist of the possible contributions on the tutorials: https://galaxyproject.github…
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Supporting a GFF file like this:
```
1 araport11 mRNA 52061 54689 . + . ID=transcript:AT1G01110.1
1 araport11 exon 52061 52730 . + . Parent=transcript:AT1G01110.1;Name=AT1G01110.1.exon1;constitutiv…
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Data in `/shared/biodata/example_data`
What are recommendations for:
- primary data storage? with SR? copy to own folders?
- large intermediate data files (SAM, BAM, etc)?
What type of directo…
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**Sorry for pasting screenshots here, just to present my confuse.**
-Python 3.9.12, whatshap 1.7
-install whatshap by pip
-`whatshap split` default parameter
The species is a diploid and the ref…
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Dear,
First of all, sorry for asking about nanopore in the first issue when it is clearly indicated that this pipeline is ment for PacBio HiFi reads.
BUT, since it takes as input the assembly a…
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**Use case**
I'm using the hmmratac implementation within MACS3 but it does not output narrowPeak.
**Describe the problem**
I'm using the hmmratac implementation within MACS3 but it does not outp…