User: dsull
dsull • 130
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Posts by dsull
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... You don't need BAM files to normalize count data with DESeq2. ...
written 11 weeks ago by
dsull • 130
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... 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
dsull • 130
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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
dsull • 130
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... 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
dsull • 130
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... 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
dsull • 130
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... 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 ...
written 3.0 years ago by
dsull • 130
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For GDC: Retrieving RNA-Seq data for Tumor vs. Matched normal tissue
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