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Recent Replies
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller?
by
zihanss
•
0
Hello, I want to know that why my gVCF files have "./." besides "0/0", "1/1"?
Thanks
Comment: gvcf joint calling
by
zihanss
•
0
![enter image description here][1]
[1]: /media/images/15eedc1a-b2c6-4966-be39-b5173dab
And I confused with the file that has "./." and…
Comment: gvcf joint calling
by
zihanss
•
0
![enter image description here][1]
[1]: /media/images/16fd502c-4e01-4f56-8562-0e0d4aac
Okay, this is the merged gVCF file.
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★
27k
Enzymes under the umbrella of `1.1.1.-` work `with NAD(+) or NADP(+) as acceptor`. That only tells you about their cofactors, but not about…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★
5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★
5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion.
As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴
520
> This is a super-interesting question from an algorithmic standpoint
Ya, I was hoping to find some algorithm that would compare say a 're…
Comment: ScRNAseq-How to correctly choose cell type marker genes
by
Francesco
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Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴
520
> My first question would be how strong your background in such analysis
> is.
Very strong. PhD+several years working in the field.
> Wot…
Comment: NGS forensics: how to know if data is fabricated
by
ATpoint
82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
Answer: absolute path for symbolic links in Snakefile
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Jesse
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740
It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
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Jesse
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740
[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
Comment: Source other conda environments in a nextflow pipeline when nextflow itself is i
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Arup Ghosh
3.2k
Use the standalone version of Nextflow and specify the process-specific conda environments paths.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
can you show us an exonic position in your VCF file that is all `./.`?
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