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Moderator: swbarnes2

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swbarnes2 ♦ 6.9k
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Posts by swbarnes2

<prev • 831 results • page 1 of 84 • next >
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Answer: A: Using ColSums vs sizeFactors in read count normalization
... For finding DE genes, you should follow the regular DESeq2 protocol and **not** use FPKM. For visualization purposes, 'correct' normalization is a little less important. Learn how each normalization works, and decide which way's assumptions better fit your data. ...
written 3 hours ago by swbarnes2 ♦ 6.9k
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Answer: A: Is it necessary to trim adaptor sequences?
... > I'm afraid that it's going to be too short for alignment (I used > SE50). If trimming adapters makes a read that aligns not align...it should not align. Trimming shouldn't hurt...but it might not help. In my experience with STAR, STAR had no problem soft trimming adapter sequences to mak ...
written 16 hours ago by swbarnes2 ♦ 6.9k
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Answer: A: How to perform strand-aware (RNA-Seq) mapping using STAR?
... STAR does not use strand information for mapping and it will output gene counts for 3 kinds of strandedness. There is no contradiction here. Just run it and look for yourself. ...
written 1 day ago by swbarnes2 ♦ 6.9k
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Answer: A: Split Fastq files
... > Does this mean that ,for each sample, the fastq has been split in 5 > parts (across each lane) and that I'll have to combine the forward and > reverse reads for each lane to get one set of fastq files for each > sample? In theory, there might be QC issues between lanes, like if there ...
written 1 day ago by swbarnes2 ♦ 6.9k
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Comment: C: samtools sort error
... `-o final output to stdout` looks like exactly what is happening. I used that ancient version for a long time, I'm pretty sure I used `> sorted.bam` ...
written 2 days ago by swbarnes2 ♦ 6.9k
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Answer: C: samtools sort error
... What version of samtools are you running? It looks like an older version that wants a ">" instead of "-o" to redirect output to a file instead of the terminal. ...
written 2 days ago by swbarnes2 ♦ 6.9k
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Answer: A: Why you shouldn't normalize count data using gene-length AND library size for co
... Another problem with normalizations like TPM and RPKM is they will flatten out the raw read counts. Let's say you have a project where one sample has a gene with TPM of 0.5, and another sample has TPM of 1.0 Do those mean something like 2 reads versus 4 reads? Or more like 40 reads versus 80 read ...
written 9 days ago by swbarnes2 ♦ 6.9k
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Comment: C: Transcripts highly constitutively expressed
... What about picking genes with low p-values and very small fold changes? ...
written 10 days ago by swbarnes2 ♦ 6.9k
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Answer: A: multiple comparisons in DESeq2
... If your contrasts work, you don't have to worry about what ResultsNames shows you. And you can submit a contrast to lfcshrink, see the example at the bottom https://rdrr.io/bioc/DESeq2/man/lfcShrink.html I don't think you need that model.matrix line in there, and I'm not sure what that all() stat ...
written 14 days ago by swbarnes2 ♦ 6.9k
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Answer: A: Extract the sequence of a gene from an aligned BAM file
... You have the # of reads in the region, what more do you want? Can't you do the division yourself? ...
written 14 days ago by swbarnes2 ♦ 6.9k

Latest awards to swbarnes2

Scholar 1 day ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 13 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 4 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 7 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 9 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 9 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 10 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 3 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 3 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 3 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Exon-Seq Mutation Detection
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 5 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 5 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 6 months ago, created an answer that has been accepted. For A: Bam to nucleotide frequencies
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values
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