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jabaron.phd
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ATpoint
76k
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Morgan S.
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paria
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marongiu.luigi
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Recent Replies
Comment: Salmon index not progressing
by
ATpoint
76k
Just wait until it is finished. It's seems to be running. I just checked my logs and on our HPC with four cores such as process for a decoy…
Comment: Salmon index not progressing
by
GenoMax
134k
> 2 hrs trying to generate decoy-aware transcriptome for human. is this time normal?
It is probably normal considering resources you have…
Comment: Chromosome bias on RNA-Seq differential gene expression analysis
by
grant.hovhannisyan
★
2.5k
you expect to have aneuploidy only in the knockout?
Comment: STAR index not working
by
camillab.
▴
130
thank you! I am following GenoMax suggestion and I am trying with `salmon` but it is stuck as well. it's not making any progress.....
Comment: Scanning for ultra-hot topics in science via pubmed, or using other tools
by
LauferVA
3.7k
@genomax , thank you. this is a really great start.
i will likely use a python based approach, but other than that, i think ill proceed e…
Comment: OMA in AWS cloud
by
Ram
40k
> if it is possible.
Yes, most things are possible on AWS.
> I didn't find anything in the web.
I *highly* **highly** doubt that.
Comment: genome data downloads for various strains
by
Ram
40k
Is there a reason you keep replying to your own messages instead of writing one complete comment and leaving it at that?
Comment: How to download genomes and proteins from JGI in bulk via the command line?
by
GenoMax
134k
You probably know about https://github.com/glarue/jgi-query already?
It is not going to be as simple to download from JGI compared to NCB…
Answer: Chromosome bias on RNA-Seq differential gene expression analysis
by
Charles Murtaugh
▴
40
If you look at all genes by chromosome, not just those that are nominally significant for differential expression, do you see an overall tr…
Comment: STAR index not working
by
Ram
40k
It gives it a better chance. It can't bypass what STAR needs but it can limit what STAR gets access to, ensuring a safe failure that does n…
Answer: Filtering VCF to divide with equal sizes
by
Pierre Lindenbaum
156k
I wrote https://jvarkit.readthedocs.io/en/latest/VcfToIntervals/ , use it to generate a set of intervals of ~10000bp for your vcf
bcft…
Comment: STAR index not working
by
camillab.
▴
130
Do you think it will make it work on my Mac that has less than 30G RAM?
Comment: Significance testing of top vs. random SNPs
by
dthorbur
▴
550
I suspect there is a more appropriate way, but you could do a permutation analysis, randomly sampling *n* SNPs 1000 times and generate a on…
Comment: STAR index not working
by
Ram
40k
Please use STAR's RAM usage options whenever you use STAR. `--limitGenomeGenerateRAM` is the relevant RAM usage parameter here.
Comment: FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of d
by
ccbb7aab4
▴
20
This looks promising, so we can apply CytoNorm before any cleaning has taken place?
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