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Recent Replies
Comment: How to convert abundance table to mean ranked abundance table in R
by
smrutimayipanda
▴
20
can you please tell me how to convert into mean ranked abundance in R language?
Comment: CPM or TPM in GSEA analysis
by
dare_devil
★
1.6k
`TPM` is `not useful` for `differential gene expression` analysis by any tool (Not only EdgeR)
Comment: CPM or TPM in GSEA analysis
by
dare_devil
★
1.6k
Simply making a comment `incorrect` do not make your statement valid. Give enough proofs to stand with your comment.
`How do TPM deals wit…
Comment: Box plots with logFC values
by
myfam128
•
0
I have seen in many research papers logFC boxplots between two conditions
example
![enter image description here][1]
[1]: /media/image…
Comment: Automated way to pull representative/RefSeq genome using full species name?
by
GenoMax
123k
Every bacterial species will likely have one strain that is used more often. e.g. Escherichia coli str. K-12 substr. MG1655 and others that…
Comment: Automated way to pull representative/RefSeq genome using full species name?
by
LChart
1.4k
I think the idea is to pull "the representative" genome. Other than maybe PAO1 for pseudomonas, I can't think of "the" representative strai…
Comment: How to interpret the nine-square plot from mageckFlute
by
ATpoint
66k
That having said, MAGeCK MLE (which FLUTE runs) calcualtes a "representative" β value for each gene as an aggregate of all shRNA/sgRNAs per…
Comment: Does this mean it is running? It has been like this for a while. I am using Trim
by
ATpoint
66k
Look, some general forum etiquette:
This is an open forum where **volunteers** try to help out each other. That means, if you post a quest…
Answer: Automated way to pull representative/RefSeq genome using full species name?
by
GenoMax
123k
There are [15507 assemblies that represent][2] 236000 prokaryotic RefSeq genome collection as of early 2022. A larger [**collection includ…
Answer: How to interpret the nine-square plot from mageckFlute
by
jared.andrews07
★
14k
Light purple means unchanged in treatment samples and decreased in control samples. Dark purple means unchanged in treatment samples and in…
Comment: Meta-analysis of gene expression data versus individual dataset analysis
by
maryam_rashidifar
▴
10
No i just need it for part of my manuscript.
The Challenge is about some additional genes in meta-analysis that were not common in all t…
Comment: CPM or TPM in GSEA analysis
by
benformatics
3.3k
This is **incorrect** since GSEA uses the gene expression **ranks** so you should use the normalized counts (e.g. TPM).
Comment: How to convert abundance table to mean ranked abundance table in R
by
LChart
1.4k
That file is giving you the abundance estimates on a per-sample (per-input-bam-file) basis. "Mean abundance" describes mean of those values…
Comment: Splitting CRAM files
by
GenoMax
123k
Yes. You could do this on the fly.
$ samtools view new.bam | cut -f1 -d$'\t' | cut -f1-4 -d$':' | sort | uniq
NS500177:19:H2HLYAF…
Comment: Splitting CRAM files
by
langziv
▴
20
So I need to convert the CRAM files to FASTQ files in order to get that information?
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