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Showing: best practices • reset

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addressing software versions

software error gatk best practices written 22 months ago by prasundutta87 • 360

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Determining the subjects to use after obtaining a PC plot of population substructure

gwas population stratification best practices written 2.5 years ago by Sheila • 310

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Forum: What are your "model" examples for bioinformatics programming?

github coding forum rna-seq best practices written 4.4 years ago by Dan D ♦ 7.0k • updated 4.4 years ago by Pierre Lindenbaum ♦ 124k

Recent Votes

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Recent Awards • All »

Scholar to Kevin Blighe ♦ 52k
Appreciated to h.mon ♦ 29k
Teacher to genomax ♦ 75k
Scholar to genomax ♦ 75k
Teacher to dariober ♦ 10k
Scholar to liorglic • 130

Recent Replies

C: Process to remove terminal Ns from fasta? by genomax ♦ 75k
OP does not want to remove a fixed number of bases but all N's. Which I assume may be of variable...
C: Help Troubleshooting FASTQC by genomax ♦ 75k
You would find it useful to read several blog posts by authors of FastQC that you can find them h...
A: Process to remove terminal Ns from fasta? by yztxwd • 240
Use seqkit subseq: example: seqkit subseq -r 6:-1 test.fa # remove the first 5 bases
C: How to Collapse Bedtools reciprocal overlap regions by Vaidhy • 0
I am trying to use this solution and there seems to be something wrong within awk; I am not getti...
A: Salmon auxiliary output by Ahill • 1.7k
See the Salmon docs: [here][1]. These are gzipped, but in a binary format which the docs describ...
C: differential expression volcano plot by Kevin Blighe ♦ 52k
What Jared says is, at the end of the day, what you likely want to do.
C: What is the Variance means in PCA plot ? by swbarnes2 ♦ 7.1k
Your p-values are meaningless, and your fold changes might be nonsense, because you have no repli...
C: differential expression volcano plot by michelle.piquet • 10
Hi Kevin, I don't understand what I'm suppose to do. How do I go about binding everything in th...
C: differential expression volcano plot by michelle.piquet • 10
I already did differential expression for both conditions, I just need to to plot them into a vol...
C: Program to find genes up/down-regulated by a given gene by c_u • 140
Hey hugo, yes! And we are planning to publish it early next year. Will upload a preprint soon and...
A: secondary structure comparison - how to approach this? / tools? by Mensur Dlakic • 2.5k
There used to be a tool for that, but it is currently unavailable: https://academic.oup.com/bioi...
C: Phasing with SHAPEIT by melania 2282 • 40
Thank you Kevin your code and explanation

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