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Recent Replies
Comment: Unusual File Count in 10x scMultiome Data for Cell Ranger ARC Processing
by
Wu-Sheng Zhang
•
0
Hi @genomax , thank you very much for your help! I go through that page but still a little confused. 10x scMultiomics data would store scAT…
Comment: multiBamSummary
by
JC
13k
check https://broadinstitute.github.io/picard/explain-flags.html to choose a proper flag
Answer: multiBamSummary
by
JC
13k
Yes, `--samFlagExclude 16` will exclude reads in the reverse strand, you need `--samFlagInclude 16` (primary hits, reverse strand) or some …
Answer: Mapping ~100-300bp Sequences to Metagenome-Assembled Genomes
by
Mensur Dlakic
★
29k
While I use Bowtie2, there is not a strong argument for it versus other genome aligners. I guess it is because I found a pipeline back in t…
Comment: How to convert CIGAR string to VCF?
by
cmdcolin
★
4.1k
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…
Comment: How to display a VCF/BCF file or stream as a paginated table in a python web fra
by
Jeremy Leipzig
23k
seqr now fully supports Hail but apparently there are some issues that will force yet another switch https://github.com/broadinstitute/seqr…
Answer: How to convert CIGAR string to VCF?
by
Pierre Lindenbaum
165k
pseudo code:
refpos1 = <something-clipped-start>
readpos0= 0;
for(CigarElement ce: cigar) {
char co = ce.getOpera…
Comment: Split genotypes in VCF file
by
Biomonika (Noolean)
3.2k
vt decompose did the trick for me, followed by the filtering for 10th and 11th column. Thanks!
Comment: CLI Downloading from Human Microbiome Project Given Login + contact failure
by
Arup Ghosh
3.3k
Try the [HMP client][1] to download files from their [new portal][2].
[1]: https://github.com/IGS/portal_client
[2]: https://portal.h…
Comment: Extract FUngal mRNA from RNAseq Data
by
SomeOne
▴
170
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…
Comment: Gini Coefficient and Lorenz curve to measure uniformity of coverage
by
abascalfederico
★
1.2k
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…
Comment: Why do people say it doesn't matter whether you run unassembled or assembled rea
by
dthorbur
★
2.8k
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…
Comment: Extract FUngal mRNA from RNAseq Data
by
GenoMax
149k
It is worth trying. You will know reads that map to the fungal reference (even though fragmented) definitely belong there.
You could also…
Comment: Extract FUngal mRNA from RNAseq Data
by
SomeOne
▴
170
unfortunatly there is no chromosoem level reference genome available. But there are some genome assemblies available at scaffold or contig …
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