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Recent Replies
Comment: Bioinformatics: what do you think of it in the next 20 years?
by
Istvan Albert
99k
10 years ago https://www.biostars.org/u/36/ told us:
>I've been doing bioinformatics for about 10 years now. I used to joke with a friend …
Comment: From TPM to raw counts
by
Istvan Albert
99k
Now that I thought about it more, you'll need the total number of reads mapped to produce the normalization factor.
You can undo the TPM o…
Comment: How Can I move the scattered dots more closer into the center of box ?
by
ohtang7
▴
40
You're right. I would get help from StackExchange sites and GPT
Answer: Is bisulfite-seq data from different studies comparable with each other?
by
NextGenSeek
•
0
The efficiency of bisulfite treatment itself can differ significantly, so I would definitely not compare bisulfite-seq data from different …
Answer: Issue with genetic QC sex check
by
kl
▴
10
After setting set-hh-missing, I have the following boxplot, where a F statistic of 0.91 corresponds to a female in my phenotypic dataset wh…
Comment: Bioinformatics
by
ATpoint
78k
Converting data from one to another format and repairing gene names turned dates. Yes, great field.
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
by
GenoMax
136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts
by
Gama313
▴
120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link:
…
Comment: From TPM to raw counts
by
Gama313
▴
120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated?
by
swbarnes2
13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
fluke
•
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…
Comment: 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/…
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