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Pierre Lindenbaum
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obidobi
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Recent Replies
Comment: Which strand specific option need to be used with HISAT2?
by
Antonio R. Franco
★
4.8k
It is very convenient to use the pseudo mapper [salmon][1] with the `-l A` option. Salmon evaluates all forms of strandness at the same tim…
Comment: Metabolomics log-transform or standardize for WGCNA
by
obidobi
▴
30
Hi Kevin,
Thanks for an excellent summary!
I have a Q related to this topic, do you think both normalizing and log transformation are re…
Comment: Parsing the codeml output in nice format?
by
sunnykevin97
▴
790
I tried this
import pandas as pd
lines = []
with open("/home/sun/Documents/genesite/Selection_Analysis/M0_res.txt", mode=…
Comment: Problem while uploading DESeq2 library
by
cpad0112
21k
That is a problem. Every time you install a package, you will have to run Rstudio as admin. Try configuring user directory for library inst…
Comment: Get number of reads with a single, (almost) exact match to the full length of a
by
GenoMax
117k
> Almost feel like using blastn might be better at this point...
Actually using a global alignment tool may be better. You could try `need…
Comment: I have sequenced 4 MRSA genomes. If I want to perform pan genome analysis for th
by
Joe
20k
Less bluntly: it depends on the question you're asking, but I can't really think of a question worth asking where only 4 genomes will satis…
Answer: I have sequenced 4 MRSA genomes. If I want to perform pan genome analysis for th
by
Joe
20k
You need more.
Comment: I have sequenced 4 MRSA genomes. If I want to perform pan genome analysis for th
by
GenoMax
117k
Posting your entire question as the title and then repeating it in the body of the post is bad etiquette. Please edit the post and post a c…
Answer: nextflow error
by
ATpoint
62k
While conda is awesome for many things, `nextflow` installation is really just `curl -s https://get.nextflow.io | bash` and done. Try that …
Comment: Comparison of two ChIP-seq experiments - impact of read length, PE or SE and cov
by
ATpoint
62k
The influence of sequencing is probably minor when it comes to read length and PE/SE. For coverage, it really depends on the quality of the…
Comment: How to retrive genomes of the isolates from specific regions? For example, If I
by
Jaykumar
•
0
Thank you very much! It worked!!
Answer: VEP annnotation on millions of variants
by
Pierre Lindenbaum
146k
+ convert your vcf to bed (eg: https://www.biostars.org/p/9506628/#9506647 )
+ annotate each region using `bcftools view --regions-file th…
Comment: Problem while uploading DESeq2 library
by
amrsalaheldin50
•
0
Solved !! by run Rstudio as adminstrator and the packages are installed smoothly.
Comment: Problem while uploading DESeq2 library
by
Basti
▴
500
Have your tried to close and reload your R session ? After you can try to reinstall
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