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Answer: How does edgeR's filterByExpr work?
C: Single rare variant approaches
C: Single rare variant approaches
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
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Recent Replies
Comment: how to get visium HD dataset with its information
by
GenoMax
145k
Depending on how much of that information is personally identifiable you may not be able to get the metadata unless you get approval from d…
Comment: HTseq count issue, not aligning to features
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GenoMax
145k
Have you examined the alignments with IGV or a similar genome browser? Are the reads aligning in correct place (e.g. under exons). Also try…
Answer: featureCounts segmentation fault
by
Mensur Dlakic
★ 28k
It is very difficult to follow al the lines as your script content are not properly formatted. It appears that in one command you are do…
Comment: Using GEOquery
by
ATpoint
84k
Have you even read my answer? I gave a full explanation on what the problem is and what the solutions can be. What is unclear?
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
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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
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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
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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
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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?
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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
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bk11
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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
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`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?
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Ram
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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
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Istvan Albert
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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
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GenoMax
145k
This blog post may partly help: https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use
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