User: jamespower

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jamespower50
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Posts by jamespower

<prev • 24 results • page 1 of 3 • next >
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Comment: C: How to best summarize read counts overlapping promoters when read counts are def
... Sorry, I cannot remap. Let me correct, thank you. ...
written 29 days ago by jamespower50
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Comment: C: How to best summarize read counts overlapping promoters when read counts are def
... Hi, my question is not how to do it but what is the best approach with overlapping read counts, which depends on assumptions on distribution of read counts: I don't know whether to sum the counts, to take the mean, the average, or do something else. Maybe this is not the best website to ask this? ...
written 29 days ago by jamespower50
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How to best summarize read counts overlapping promoters when read counts are defined from different regions
... Hi, I have read counts from a dataset (dataset1) that are defined from regions of 100 bases, and I am trying to find the best way to get a one value (read counts value) for each promoter region (of 1000 bases). In particular, how to treat read counts in overlapping regions? I know there is a lot ...
gene assembly next-gen chip-seq rna-seq written 29 days ago by jamespower50 • updated 29 days ago by geek_y11k
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Answer: A: List of TCGA genes differentially expressed in normal versus tumor
... To follow-up if useful to others, I found three websites that will do this automatically: http://gepia.cancer-pku.cn/index.html xena.ucsc http://www.cbioportal.org/ The gepia website seems great because it allows to do a bulk comparison, the others seem to be focused on a "by gene" comparison. ...
written 5 weeks ago by jamespower50
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Comment: C: List of TCGA genes differentially expressed in normal versus tumor
... Thank you Kevin for your reply. Yes, time constrains, and the fact that I was hoping there were gene lists available already, since it seems like a very common and possibly simple analysis that doesn't need to be re-done by everyone... ...
written 15 months ago by jamespower50
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List of TCGA genes differentially expressed in normal versus tumor
... Hi, I am looking for a gene list with differentially expressed genes in a particular tissue, using normal versus tumor samples (for example as reported in https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071462#s3). The TCGA website has RNA-Seq data on tumor samples, but I was j ...
tcga rna-seq written 15 months ago by jamespower50
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Comment: C: Plink Error: Duplicate ID 'chr:pos:A1:A2' generated by --set-missing-var-ids
... Thanks! Using plink2, with `--set-missing-var-ids @:#\$r:\$a`, and `--new-id-max-allele-len 23 missing` works great! ...
written 16 months ago by jamespower50
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Plink Error: Duplicate ID 'chr:pos:A1:A2' generated by --set-missing-var-ids
... Hi, I am trying to work with the 1000Genomes data starting from the vcf file, which has missing IDs. So, I thought of adding the flag `--set-missing-var-ids @:#:\$1:\$2`, but this gives me the error: Error: Duplicate ID generated by --set-missing-var-ids. So I guess first we want to find ...
duplicates missing id plink written 16 months ago by jamespower50 • updated 16 months ago by RamRS27k
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How to combine RNA-Seq from Novaseq separated in lanes, after fpkm have been computed?
... Hi, I have been given two files with FPKM values computed on different lanes for the same sample, is it appropriate to sum the FPKM values by gene and sample across the different lanes? Thank you for any help ...
gene next-gen rna-seq written 17 months ago by jamespower50
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Comment: C: Format in vcf files in Geuvadis data not recognized
... Even if it says it as a warning, I cannot do certain operations such as extracting sample IDs (I update the last output for the error message). ...
written 23 months ago by jamespower50

Latest awards to jamespower

Student 20 days ago, asked a question with at least 3 up-votes. For Compute confidence intervals for lambda genomic factor statistics
Popular Question 5 weeks ago, created a question with more than 1,000 views. For QQ plots for eqtl data
Popular Question 15 months ago, created a question with more than 1,000 views. For QQ plots for eqtl data
Popular Question 15 months ago, created a question with more than 1,000 views. For Compute confidence intervals for lambda genomic factor statistics
Popular Question 15 months ago, created a question with more than 1,000 views. For Plink associations using covariates as numeric or dummy

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