User: jtull

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jtull0
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Posts by jtull

<prev • 11 results • page 1 of 2 • next >
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Answer: A: need annotation file
... Try this https://www.gencodegenes.org/human/ ...
written 12 days ago by jtull0
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Comment: C: Batch effect correction
... Thank you very much. ...
written 13 days ago by jtull0
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Comment: C: Batch effect correction
... I see, thanks. Any suggestions though, e.g. sva package? Also, when I use design = ~ condition, I still get some of the genes from the initial list as differentially expressed. Do you think the analysis still has some meaning to it or we cannot do the DE analysis at all? ...
written 13 days ago by jtull0
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Comment: C: Batch effect correction
... Yes, they are from the same batch. ...
written 13 days ago by jtull0
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Batch effect correction
... Hi, I am interested in human validation of a set of genes identified as differentially expressed between 2 groups in mice and for that, I am using some control samples from a publication. I've read that to remove batch effects with DESeq2, introducing the batch in the design of the experiment as de ...
rna-seq differential gene expression batch effect written 13 days ago by jtull0 • updated 13 days ago by swbarnes29.2k
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TCGA RNA-seq data from blood derived normal
... I want to download RNA-seq data (bam files) for the available blood derived normal samples from the TCGA (any cancer site). I believe there are some, though very few. How can I generate a list of barcodes for these samples? Thanks! ...
tcga rna-seq written 7 months ago by jtull0
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Comment: C: Suspicious TCGA tumor samples
... Yes, from COAD, not PRAD. Sorry about the confusion. Thanks for your suggestions. ...
written 10 months ago by jtull0
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Comment: C: Suspicious TCGA tumor samples
... Sure, a couple of them for instance from the TCGA PRAD: TCGA-A6-5659-01B-04D-A274-01, TCGA-D5-6930-01A-11D-1923-01, TCGA-DM-A1HB-01A-21D-A182-01, TCGA-78-8648-01A-11D-2389-01, TCGA-86-A4P8-01A-11D-A24O-01, TCGA-L4-A4E6-01A-11D-A24C-01, TCGA-56-8623-01A-11D-2391-01, TCGA-85-A4PA-01A-11D-A256-01, TCGA ...
written 11 months ago by jtull0
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Suspicious TCGA tumor samples
... I am analyzing a set cancer sites from the TCGA and I came across some samples that have no copy number aberrations throughout the genome. I assume that's possible for some but for some cancer sites, the number of those just seems more than I'd expect. So, my question is, is there a way to check for ...
tcga the cancer genome atlas written 11 months ago by jtull0
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Comment: C: Splitting genomic intervals based on chromosome arm
... Thank you, it works just as I wanted! Just a note, maybe add rm interval.*[pq] in the end of the bash script to clean up the temporary interval files. ...
written 12 months ago by jtull0

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