Moderator: igor

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igor6.2k
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Posts by igor

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Answer: A: Filtering rRNA from RNAseq data
... There are some related suggestions in this previous thread: https://www.biostars.org/p/207311/ ...
written 3 days ago by igor6.2k
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Comment: C: Estimating cross contamination in a set of BAMS
... I didn't realize there is a manual for CalculateContamination. That's helpful. ...
written 3 days ago by igor6.2k
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Answer: A: how to make this plot for mutation in paired samples?
... OncoPrinter (web-based): http://www.cbioportal.org/oncoprinter.jsp ![enter image description here][1] ComplexHeatmap oncoPrint() function: https://github.com/jokergoo/ComplexHeatmap ![enter image description here][2] [1]: https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/ima ...
written 3 days ago by igor6.2k
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Answer: A: Estimating cross contamination in a set of BAMS
... A really nice method is [GATK CalculateContamination][1] and gives you an exact contamination estimate. It works if you have WGS/WES data (to provide sufficient coverage for enough SNPs). They provide a reference VCF for human genome. It needs to be in a specific format, so can be tricky to generate ...
written 3 days ago by igor6.2k
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Comment: C: Single Cell mRNA Seq basic question
... I have seen estimates of 500k transcripts. It will vary by cell type, though. And, as others have pointed out, one transcript can produce multiple reads. ...
written 7 days ago by igor6.2k
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Answer: A: TCGAbiolinks TCGA-BRCA RNA-seq clinical data
... You could also consider using the Pan-Cancer Atlas curated survival data from Xena: - [Survival_SupplementalTable_S1_20171025_xena_sp][1] [1]: https://xenabrowser.net/datapages/?dataset=Survival_SupplementalTable_S1_20171025_xena_sp&host=https%3A%2F%2Fpancanatlas.xenahubs.net ...
written 10 days ago by igor6.2k • updated 9 days ago by zx87544.5k
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Comment: C: Analysis ready RNA Seq repository
... Looks really nice. Can I suggest adding normalized values in addition to the raw counts? Since you have all the downstream analysis, I assume they are already calculated. That way, users can check the expression pattern of their favorite gene. In my experience, that would be very valuable. ...
written 10 days ago by igor6.2k
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Answer: A: How to know the mm9 genome size?
... For MACS, genome size is already precompiled for common species. No need to do extra work. You can use `mm` for mouse. This is explained in more depth in the [documentation][1]. [1]: https://github.com/taoliu/MACS ...
written 11 days ago by igor6.2k
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Answer: A: ATAC-seq macs2 peak calling bampe mode extension shift
... According to the MACS developer: > If you followed original protocol for ATAC-Seq, you should get > Paired-End reads. If so, I would suggest you just use "--format BAMPE" > to let MACS2 pileup the whole fragments in general. But if you want to > focus on looking for where the 'cutting s ...
written 13 days ago by igor6.2k
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Comment: C: Any tools for predicting binding affinity between TCR and epitode?
... Thanks for clarifying. IEDB has a lot of different tools, so I assumed they covered the full range. Maybe not. ...
written 14 days ago by igor6.2k

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