User: theodore.killian

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Posts by theodore.killian

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Variant Calling scRNA-seq data for KRAS mutations
... We use 10X. I was thinking of using FreeBayes on the aligned reads, although I know that the called SNPS are strongly contingent on the read depth. ...
written 9 days ago by theodore.killian0
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Variant Calling scRNA-seq data for KRAS mutations
... I have sequenced scRNA-seq data and I would like to do variant calling for one gene (KRAS) so I can annotate clusters in the downstream analysis. I have looked at past posts and there doesn't seem to be a lot of consensus on what tools to use. However, I understand that I would do something like: 1 ...
rna-seq snp written 9 days ago by theodore.killian0
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Why don't all GOIDs and all ENTEZIDs appear in db query?
... I want to get all GO terms for a particular organism. Additionally, I want to get all of the ENTREZIDs My problem is that (for example) GOID GO:0032501 *does not appear* in the list from the query below: ``` go_list <- mapIds(org.Hs.eg.db, keys(org.Hs.eg.db, "GO"), "ENTREZID", ...
R written 5 months ago by theodore.killian0
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mapIDs function not obtaining all GOIDs for organism
... I've been performing GO enrichment using limma::goana on RNAseq data analyzed with DESeq2. The results is a list of enriched GOIDs. Additionally, I wanted to get all the ENTREZIDs for each differentially enriched GO term found in the results. I went about doing this by trying to get all GOIDs and al ...
R go rna-seq written 5 months ago by theodore.killian0
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Answer: A: Msc in bioinformatics at Gent University
... I graduated from the KUL Bioinformatics program last year. It's relatively easy to do a master's thesis in industry (and potentially get paid). You can do a industry thesis potentially anywhere, although it's incumbent on you to do the legwork of finding a suitable company. I don't know about the U ...
written 16 months ago by theodore.killian0
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Comment: A: Is computing TPM from read count from DEseq2 count matrix necessary?
... I have obtained the transcript lengths of the genes from my count matrix. Do I use the mean transcript length to calculate TPM? ...
written 16 months ago by theodore.killian0
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Is computing TPM from read count from DEseq2 count matrix necessary?
... I am building an RNAseq pipeline using DESeq2 to show transcriptional differences between a group of RNAseq samples starting from a raw count matrix. Is calculating TPM (from the raw count matrix) unnecessary in this context when I already have the normalized counts produced by the DESeq2 analysis? ...
gene R rna-seq written 16 months ago by theodore.killian0

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