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Marco Pannone
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Pierre Lindenbaum
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Recent Replies
Comment: Ribosomal Depletion
by
andres.firrincieli
★
2.5k
It is easier and do his job. But if you are planning to do differential expression then follow @grant.hovhannisyan suggestion
Comment: Ribosomal Depletion
by
grant.hovhannisyan
★
2.4k
then I recommend not bothering about removing the rRNA data during the mapping - just map all your data to the entire reference, do the cou…
Comment: Ribosomal Depletion
by
kcarery
•
0
Why do you recommend? Is it easier? From my understanding, STAR is the best aligner
Comment: Ribosomal Depletion
by
kcarery
•
0
I am planning to generate counts to do differential expression and pathway analysis
Comment: Ribosomal Depletion
by
grant.hovhannisyan
★
2.4k
what downstream analysis are you planning to do after getting the non-rRNA bam file?
Comment: Ribosomal Depletion
by
andres.firrincieli
★
2.5k
Instead of STAR use [bbduk.sh][1] from [BBmap][2]
[1]: https://www.biostars.org/p/159959/
[2]: https://sourceforge.net/projects/bbmap/
Comment: Exctract unmapped reads from BLAST
by
Pilar
•
0
Thank you very much. I've used `-outfmt 7` repeating my blast step. I'm working with a huge database, so it's going to take many hours to f…
Comment: Exctract unmapped reads from BLAST
by
Pilar
•
0
Thank you very much for your quickly response. The `comm` command has been very useful :) I figure I have the output file I needed.
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
If 1kgtot.bim contains doubled IDs (e.g. "HG00096 HG00096", you need to provide a doubled ID to `--indv`. The log file shows that your scr…
Answer: ESTIMATE tumor purity
by
JACKY
▴
10
Just in case anyone faces this problem in the future, here is the link for the updated `estimate package` on github:
https://github.com/…
Answer: Exctract unmapped reads from BLAST
by
GenoMax
117k
> Is there a way to tell blast to output the unmapped reads into a
> separate file?
No there is not. You will need to use `-outfmt 7` whe…
Comment: Resfams Database usage
by
Neel
▴
10
Hi, i have annotated genome by prokka and o want to search amr agaisnt resfams could you please tell me how to do it steps by steps.
Comment: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
those are two distinct commands https://linux.die.net/man/1/comm and https://linux.die.net/man/1/join
extract the names of your queries, s…
Comment: Exctract unmapped reads from BLAST
by
Pilar
•
0
Thanks for answering :),
sorry, I'm new at this. These are commands I should use when I launch Blast in terminal?
Answer: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
have a look at `comm` or `join`.
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