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Comment: How to convert CIGAR string to VCF?
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cmdcolin
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i think this is a good exercise (I wrote a quick code that I have used for cigar parsing in javascript https://cmdcolin.github.io/posts/202…
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seqr now fully supports Hail but apparently there are some issues that will force yet another switch https://github.com/broadinstitute/seqr…
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pseudo code:
refpos1 = <something-clipped-start>
readpos0= 0;
for(CigarElement ce: cigar) {
char co = ce.getOpera…
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vt decompose did the trick for me, followed by the filtering for 10th and 11th column. Thanks!
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Try the [HMP client][1] to download files from their [new portal][2].
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Comment: Extract FUngal mRNA from RNAseq Data
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SomeOne
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i used the following command. Kindly let me know if i missed something or if it is now correct
```
bbsplit.sh ref=human_GRCh38.p14_genomic…
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Thank you! I finally used some code from my supervisor for the Lorenz curves, it's relatively easy, and DescTools::Gini to compute the gini…
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I'm not all that familiar with your field of research, but it would seem counterproductive to try and assemble reads of a microbial communi…
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It is worth trying. You will know reads that map to the fungal reference (even though fragmented) definitely belong there.
You could also…
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unfortunatly there is no chromosoem level reference genome available. But there are some genome assemblies available at scaffold or contig …
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If the genome for the fungus is available then you can use binning approach with `bbsplit.sh` from BBMap suite. This will allow you to logi…
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I was using it for a project where I'm trying to see the difference in abundance of SCFA-producing bacteria across microbiomes of different…
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Remember that RNA-seq data are compositional, and you can't treat the count data as absolute expression values.
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Why do you think ALL the .phe file IDs match those in the .fam file?
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