User: swbarnes2

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swbarnes2170
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Posts by swbarnes2

<prev • 38 results • page 1 of 4 • next >
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Answer: A: biomaRt returns all NAs for hgnc_symbol
... Not like this. You want to find human orthologs for those mouse symbols. You might need to go symbol -> ensembl ID -> human orthologs (which won't be 1-1) ...
written 1 day ago by swbarnes2170
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Comment: C: Log2(RPKM) counts in Bioconductor
... Short answer...throw away your RPKM values. No differential expression software wants them, and converting back to the desired raw gene counts is extremely hard to reverse engineer 100% accurately. ...
written 20 days ago by swbarnes2170
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Comment: C: Compare and filter two BAM files, one record at a time
... Isn't the usual way to do this to align to a combined human/mouse genome, and then filter for the reads that align better to one genome or another? ...
written 23 days ago by swbarnes2170
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Comment: C: Appropriate experimental design for differential expresion
... Does it make biological sense for you to lump the or's and fb's together? I'd also strongly recommend making your condition file in Excel; because you listed the fibro samples first, but you keep putting the co condition first in your condition data ...
written 4 weeks ago by swbarnes2170
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Comment: C: model design in rna seq - deseq2
... If the poster specifies the contrast explicitly, I don't think the order of person + time matters. ...
written 4 weeks ago by swbarnes2170
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Answer: A: Appropriate experimental design for differential expresion
... You are planning this experiment? You haven't done anything yet? Do not prep all your samples on three different days. Prepping all samples of one type on one day is the worst thing you could possibly do, it will make your results almost meaningless. The best thing to do would be to do all the R ...
written 4 weeks ago by swbarnes2170
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Answer: A: Find the expected counts in DESeq2 output
... counts(dds, normalized = TRUE) ...
written 5 weeks ago by swbarnes2170
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Answer: A: What are the methods to get count data per cell from single cell fastq given onl
... If you want a pipeline that goes from fastqs to gene counts that is less of a black box than 10xGenomics Cellranger, you can use what the McCarroll lab cooked up for Drop-seq https://github.com/broadinstitute/Drop-seq/releases The principle is pretty much the same; get alignments, gene assignments ...
written 6 weeks ago by swbarnes2170
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Answer: A: Simple csv import error
... You need to look hard at all the elements in your command line, and figure out what each of them is doing. Because the field separator in a csv is not white space. It's a comma. And are you sure that you want to be both skipping a row and have a header row? I get that error if I put nonsense in ...
written 7 weeks ago by swbarnes2170
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Answer: A: Appropriate design formula for DESeq2 from principles
... AFAIK, the ordering of terms doesn't matter if you specify the contrast you desire in your results statement. ...
written 10 weeks ago by swbarnes2170

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