Moderator: karl.stamm

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karl.stamm3.9k
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Posts by karl.stamm

<prev • 531 results • page 1 of 54 • next >
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Comment: C: How to handle duplicate row names in R
... Probably a transcript-level file has multiple rows for a gene with multiple transcripts. Leave it in the ID of your original file. ...
written 6 days ago by karl.stamm3.9k
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Answer: A: How to map reads onto human hg38 gene body regions instead of whole genome?
... Can't say if it's a good idea or not, but the way I would do that is to mask the genome reference. Just hack up your genome reference to have a bunch of NNNN in the intergenic regions. Or use a transcriptome mapper like STAR/RSEM directly, and forego the genome mapping. ...
written 8 days ago by karl.stamm3.9k
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Answer: A: Loading Matrices of 10X Genomics failed
... Check your file type, gzip.open did not find a csv file. ...
written 12 days ago by karl.stamm3.9k
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Comment: C: During RNA-seq analysis a lot of pseudogenes come up as DE
... you might also want to filter for absolute expression. fold-change is not well defined when one sample or the other has nearly zero expression. I've seen this effect and while it could be real, we chalked it up to technical artifact: sample processing in the wetlab caused one sample type to lose lo ...
written 12 days ago by karl.stamm3.9k
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Comment: C: What are the 5 biggest challenges/ opportunities in Bioinformatics going into 20
... Ranking open problems by 'biggest challenge' is a tough one for me. Some centers have service problems, how to get WGS results or cancer somatic variants detected ASAP. Those don't rank against scientific advancements like 3d chromatin orientation or protein docking. ...
written 17 days ago by karl.stamm3.9k
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Comment: C: Is there a tool to predict if a missense variant causes a loss of function on th
... Interested if you find one. I don't think it's well defined. We can predict if the protein will be significantly different, but whether that's good or bad depends on the whole animal and environment. ...
written 28 days ago by karl.stamm3.9k
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Comment: C: A question on the interpretation of a PCA plot
... In a true PCA, each PC is a linear combination of all genes. The genes with significant loading are probably different but there's going to be some contribution of the same genes in both PC1 and 2. One could take the definition (loading) of PC1 and PC2 and work out the difference in the groups (lo ...
written 4 weeks ago by karl.stamm3.9k
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Comment: C: Optimal Number of SNPs in NA12878 WES Data
... You havent said what the problem is. An advisor said that's too many? For some purposes you may need a top ten list; if you were diagnosing a rare disease using WES then you want to find the SNV that are not common in the general population, and maybe filter to keep only the most deleterious pro ...
written 4 weeks ago by karl.stamm3.9k
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Comment: C: Optimal Number of SNPs in NA12878 WES Data
... What seems to be the problem? True positives was 1.3 million according to NIST. ...
written 5 weeks ago by karl.stamm3.9k
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Comment: C: Mapping transcriptomes against each other to find genetic differences
... Building a reference genome for a species that doesn't have one is a pretty big task for an 'honors thesis project'. Further, using it for a three-way differential expression analysis is another big complicated project. Good luck! Building a genome from RNA-Seq is yet another difficult task. Ma ...
written 6 weeks ago by karl.stamm3.9k

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Teacher 4 months ago, created an answer with at least 3 up-votes. For A: PLINK: Not sure how to go about creating the "mylist.txt" file for the --update
Scholar 14 months ago, created an answer that has been accepted. For A: multithreading in psiblast
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