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Answer: Importing data from GEO
Importing data from GEO
A: 0 Features for COVID-19 ExpressionSet through GEOQuery
0 Features for COVID-19 ExpressionSet through GEOQuery
Comment: trying to use the API for edirect tool (NCBI)
Using GEOquery
Answer: The Evolution of NGS: What’s New and What’s Next?
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Recent Replies
Comment: Using GEOquery
by
Rohulla
• 0
I also come up with this problem. No body still answer this question.
Answer: Performing Needleman-Wunsch Global Alignment for multiple mutant proteins agains
by
Istvan Albert
101k
You can use the `bio` with the `align` tool. Install with `pip install bio` then bio align query.fa target.fa You can put all the tar…
Answer: Long-read sequencing data simulation using CAMISIM
by
Istvan Albert
101k
Since they explicitly have a pbsim config file, the comment you found is probably just a leftover from another config file that was copied …
Comment: RNA-Seq mutation calling without germline data
by
marionette.kent
• 0
Thanks @shred for sharing your pipeline. Can I ask if it runs each sample individually? Our HPC has limited space for each user so I have b…
Comment: Pedigree information
by
bk11
★ 3.0k
Since you have plink (bed/bim/fam) files, sex information is stored in the 5th column of the `.fam` file. If that information is missing an…
Comment: The Evolution of NGS: What’s New and What’s Next?
by
i.sudbery
20k
I know its a technical possiblity. But people I know that do this say its still very much an experimental technique. You need to learn the …
Answer: Merging bfiles
by
bk11
★ 3.0k
If you have common set of SNPs between your two set of bfiles `(PLINK files)`, you can use `plink --bmerge` command to merge them as follow…
Comment: The Evolution of NGS: What’s New and What’s Next?
by
Istvan Albert
101k
`rust` was not designed to be a competitor to `python`, it was designed as a competitor to `C` and `C++` - `rust` integrates really well…
Comment: Can someone install me (remotely) Amber24?
by
Ram
44k
Do you mean you have a Windows machine that has Windows Subsystem for Linux and you're unable to install a piece of software over a remote …
Comment: Choosing the Best Method for DEG Analysis: limma vs. DESeq2 for RSEM Normalized
by
Istvan Albert
101k
Fundamentally these types of filterings come down to the effect they have on the data. Does your filtering change the data, does it chang…
Comment: Generally how are non-canonical chromosomes treated in human variation studies
by
GenoMax
145k
This blog post may partly help: https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use
Comment: Why does assigning genes with biomart give me different values than using a tran
by
bioinfo
▴ 150
Do you think that I should be including the information from the scaffold patch for the quantification? Initially I used the transcript_to_…
Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
by
GenoMax
145k
It has been moved to a comment (looks like you are a moderator that seems to have come back after a long break). You can accept @dgtool ans…
Answer: Mendelian precison
by
Pierre Lindenbaum
164k
For trios and short-reads, I use delly or manta to get a join VCF of the trio (+ a few controls to discard false positives). I then kee…
Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
by
Ian
6.1k
Thank you your suggestion on using -O worked. Makes sense in hind-sight. Sorry I couldn't select your answer as the "winner" as you poste…
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