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Comment: Repeated testing/data mining in RNA Seq
Comment: UMI-Tools knee-method has great influence on the results of white list
A: LogFC and LogCPM
Comment: Help with running egsea()
removeBatchEffect explained using base R linear models
Comment: Help with running egsea()
Why employ normalization methods, and how can they be utilized in DEG analysis?
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Recent Replies
Comment: ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG lin
by
GenoMax
142k
> I don't understand why SAM header has "Duplicate entry" and what should I do in this case. Your reference sequence must have fasta head…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
I can't immediately see anything wrong. The log file should contain lines saying how many reads were parsed, how many reads matched the bar…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
Thank you for the explanation. I can see the plots look strange, but i truly don't know why this is. I have a feeling that the sequencing …
Comment: High Malat-1 expression in single cell data
by
dsull
★ 6.0k
No -- those are ribosomal proteins, not rRNAs.
Comment: trying to count a pattern in my fastq file using bbduk
by
GenoMax
142k
Thanks for that link. As noted in that example, you can try `seal.sh` instead of `bbduk.sh`. > Is it possible, that this pattern is just …
Comment: Question regarding WGCNA
by
deepak
• 0
These are independent biological replicates
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
I didn't mean to sound like I was taking it as a criticism, I genuinely meant that we never intended to be a foolproof whitelisting tool. T…
Comment: Help with running egsea()
by
Chris
▴ 270
Thanks 1769mkc! I also tried fgsea. The author of limma comment on this post that p value from fgsea is not truly significant as it is http…
Comment: trying to count a pattern in my fastq file using bbduk
by
Assa Yeroslaviz
★ 1.8k
yes it does. As far as I understand it, you can use `N` here. I took it from [this example][1] Brian posted a few years ago This is why…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
thanks for the answer. I wasn't complaining about the tool (or the results for that matter). I'm just trying to understand why the differe…
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
"c2 gene set from MSigDB." this i agree in that case https://bioconductor.org/packages/release/bioc/html/fgsea.html you can try this one wh…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
If you can post the knee plot, that might be helpful. But I will add that the whitelist command in UMI-tools was primarily designed to be a…
Comment: Help with running egsea()
by
Chris
▴ 270
Thanks 1769mkc! I tried this tool. Gene expression of 2 groups is just slightly different (not hundred of differential express genes). The …
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
https://metascape.org/ this is one of the ways to make life easier if you have the genes already from the differential list
Comment: RNA editing sites based on DNA seq and RNA seq
by
Ahiad Chen Zion
• 0
In those unaligned reads, I am looking for hyper-editing. But the alignment should be much higher
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