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beausoleilmo
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Brian Bushnell
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Recent Replies
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
fluke
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0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts
by
Istvan Albert
99k
In principle, the TPM formula can be reverted, see the timeless post
* [What the FPKM? A review of RNA-Seq expression units][1]
In p…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
beausoleilmo
▴
560
You're right, I wasn't explaining the problem clearly. Thanks for the directions!
- The depth; coverage ~3.00X ± 2.50 SD
- The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★
25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
CTLong
▴
20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC
by
ayasu
•
0
Sorry for the delay in expressing my thanks.
I found the advice to look at the information from MySQL very useful.
I will also refer to t…
Comment: From TPM to raw counts
by
Brian Bushnell
19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Brian Bushnell
19k
In most cases error-correction should take care of error-spawned fake minor alleles, though...
> If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★
25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
Brian Bushnell
19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters?
by
AMARU
•
0
Can you post the commands you used?
I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
Comment: "MethylKit" package for WGBS data
by
viveksomya123
•
0
Why I am getting this histogram of CpG coverage using methylkit, is this the failure of bisulfite library preparation![enter image descript…
Comment: Should I scale all genes in single cell Seurat?
by
synat.keam
▴
80
Thanks, António for your kind and detailed responses. You helped clear my doubt about scaling!
Kind Regards,
Synat
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Brian Bushnell
19k
It's not a silly question! And yes, it can be done. JGI is currently testing various binning tools to try to find the best protocol for t…
Answer: GO categorization
by
geneontologyhelp
▴
290
[We have this in our FAQ][1]. PANTHER version 18.0, which powers the enrichment analysis on our homepage, has [143 species][2] loaded and …
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