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jabaron.phd
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ATpoint
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Morgan S.
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paria
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marongiu.luigi
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Recent Replies
Answer: Simulate short-read RNA-seq data from long-read RNA-seq data
by
Mensur Dlakic
★
24k
I think you could try doing this, but it wouldn't be appropriate. You'd be bringing long-read errors, which I believe are higher than short…
Comment: Salmon index not progressing
by
camillab.
▴
130
I opened tow terminals and one was the code to build a decoy-aware transcriptome and the other was building indexes (no decoy)
Comment: Adding a control sample to bulk RNA-seq
by
Chris
▴
180
Thank you for the explanation! So just want to confirm one control with replicate is totally useless even can't use as a reference?
Answer: DESeq2 analysis using two featureCounts generated from different studies
by
swbarnes2
13k
Comparing samples between labs is a bad idea. Better to generate gene lists from one study from one lab, and gene lists from another study…
Comment: Adding a control sample to bulk RNA-seq
by
swbarnes2
13k
If a sample wasn't prepared along side your treated samples, it is a different batch. If you had treated and controls in each of two diffe…
Comment: kallisto normalized TPM values without bootstraps
by
ATpoint
76k
You don't need sleuth. Typically these deconvolutions, or most downstream analysis, is done on the gene- rather than the transcript-level w…
Comment: Salmon index not progressing
by
ATpoint
76k
If the top $CPU column shows some values in the hundreds then it is doing something (actually when it's > 0%). So based on the screenshot i…
Comment: Salmon index not progressing
by
camillab.
▴
130
Thank you. Waiting it's not gonna hurt me, when should I stop hoping and give up is the question? do you know is there a way if I can see i…
Comment: Filtering VCF to divide with equal sizes
by
Ram
40k
A more efficient way would be to make a 2 column CSV file, one column with the count value and the other with the chr:start-end range, then…
Answer: Filtering VCF to divide with equal sizes
by
avelarbio46
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30
I divided my contigs using R, but it was more complex than the program Pierre Lindenbaum made (https://jvarkit.readthedocs.io/en/latest/Vcf…
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…
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