User: dsull

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dsull130
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Posts by dsull

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Looking for some feedback on my TCGA survival analysis approach. Any glaring fla
... You don't need BAM files to normalize count data with DESeq2. ...
written 11 weeks ago by dsull130
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Comment: C: Looking for some feedback on my TCGA survival analysis approach. Any glaring fla
... I personally think HTseq-count is fine. FeatureCounts is slightly better (especially for paired-end reads) but it's not really that significant that it's worth your effort to get the raw .bam files. I suppose an issue could be batch effects (but those are kinda hard to deal with in TCGA, and most p ...
written 11 weeks ago by dsull130
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Comment: C: Map genes to the ids
... biomaRt works great as previously suggested. Here's another tool that I often find useful for converting between gene symbols, IDs, etc.: https://biodbnet-abcc.ncifcrf.gov/db/db2db.php ...
written 12 weeks ago by dsull130
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Answer: A: How to compare different groups p value and fold change
... Hi! It seems that you have Case vs. Control and Treated vs. Untreated as your groups. What question are you trying to answer? 1) Are you trying to see what genes are differentially expressed in treated compared to untreated? You'd have a fold change: [treated] / [untreated]. 2) Are you trying to s ...
written 12 weeks ago by dsull130
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Answer: A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
... Hi everyone, After looking around, it seems that a few people are having similar problems. So, I contacted GDC and they responded very quickly and helped me find a solution, which I'm posting here in hopes that it well help someone in the future :) Here's how you do it: 1) Select all the files yo ...
written 3.0 years ago by dsull130
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GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
... TCGA has recently migrated to the Genomic Data Commons (GDC). Following this migration, many tools convenient for retrieving TCGA data, such as TCGA-Assembler, no longer apply. So, with the new GDC, I'd like to download RNA-Seq data (in bulk) for tumor samples as well as normal control samples. How ...
tcga gdc written 3.0 years ago by dsull130

Latest awards to dsull

Great Question 7 months ago, created a question with more than 5,000 views. For GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Appreciated 18 months ago, created a post with more than 5 votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Good Question 18 months ago, asked a question that was upvoted at least 5 times. For GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Popular Question 2.8 years ago, created a question with more than 1,000 views. For GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
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