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Recent Replies
Comment: How to map and annotate gene symbols to gene type?
by
GenoMax
125k
Yes it should. Look for `biotypes` ([LINK][1]).
[1]: https://www.ensembl.org/info/genome/genebuild/biotypes.html
Comment: How to map and annotate gene symbols to gene type?
by
mohammedtoufiq91
▴
170
@genomax thank you. Does this works in `biomart` R package too?
Answer: How to map and annotate gene symbols to gene type?
by
GenoMax
125k
Use BioMart at [**Ensembl**][1]. Choose `Attributes` as needed.
![enter image description here][2]
[1]: http://www.ensembl.org/in…
Answer: BLAST reference genome indexing
by
GenoMax
125k
`makeblastdb` is creating the index from `mydb.fsa` (which is your reference) file. This results in the set of files you name above. `mydb`…
Answer: command line - how to change name of multiple files at the same time
by
shenwei356
7.8k
Try [brename](https://github.com/shenwei356/brename), it's safe and powerful. also read this post: https://www.biostars.org/p/9487877/
…
Comment: batch renaming FASTQ files
by
shenwei356
7.8k
The `brename` version should be
brename -p '^(\w+?)_.+([12]).fastq.gz$' -r '${1}_$2.fastq.gz'
Answer: rDGIdb - VCF input error using locateVariant command (VariantAnnotation)
by
Gaurav
•
0
I think the issue is that the `seqlevels `do not match. Apparently, one should be a subset of the other. You could try restricting only to …
Comment: Methods for downsampling coverage in a VCF
by
Medhat
9.5k
I do not know how you want to downsample vcf file,. However, to downsample reads, you can use `seqtk sample` https://github.com/lh3/seqtk …
Answer: Error: ##fileformat=VCFv4.2 does not exist
by
sbstevenlee
▴
480
I would also recommend checking out a different star allele-calling tool named PyPGx (see [docs](https://pypgx.readthedocs.io/en/latest/rea…
Answer: command line - how to change name of multiple files at the same time
by
cfos4698
▴
570
I prefer the `rename` tool. I think you might need to install it with either something like `apt` (ubuntu), or `conda` (Linux, Mac, Windows…
Answer: Extract species-specific SNPs from VCF files
by
cfos4698
▴
570
If I'm interpreting you correctly, you want to compare the VCF files, ignore SNPs shared by two (or more) species, and instead retain only …
Comment: Issues With Using Singularity In Order To Run Software "quested access to the re
by
Indira
•
0
Thank you I realized that the mistake I made was by not making a docker image.
Comment: intersect VCF files
by
Ram
38k
Which ID and QUAL values do you pick for the output VCF record? That choice makes the difference.
Answer: Database with gene family annotations
by
Mensur Dlakic
★
22k
> I've queried the Panther database, but unfortunately it does not return annotations for all of my genes.
For any reasonably-sized quer…
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