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Recent Replies
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
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GenoMax
136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts
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Gama313
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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:
A= …
Comment: From TPM to raw counts
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Gama313
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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?
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swbarnes2
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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
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fluke
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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
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Istvan Albert
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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
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beausoleilmo
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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
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Mensur Dlakic
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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
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CTLong
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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
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ayasu
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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
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Brian Bushnell
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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
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Brian Bushnell
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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
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Mensur Dlakic
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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
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Brian Bushnell
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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?
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AMARU
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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…
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