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Moderator: swbarnes2

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swbarnes2 ♦ 7.5k
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Posts by swbarnes2

<prev • 931 results • page 1 of 94 • next >
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Answer: A: BWA-MEM read groups usage
... Many moons ago, I did a lot of variant calling with a simple mpileup-based pipeline. That software can take a list of separate bam files and call the SNPs all together. I didn't need read groups. However, I learned when I wanted to use a different software, FreeBayes, that that software doesn't t ...
written 2 days ago by swbarnes2 ♦ 7.5k
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Answer: A: Explaining relation of WGS and transcriptome
... There might be a few explanations. Off the top of my head, I could imagine a partial deletion impairing function, and the cell trying to compensate by attempting to transcribe more of it. More transcription in this case not leading to more functional protein operating. You might look at downstrea ...
written 3 days ago by swbarnes2 ♦ 7.5k
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Answer: A: Unbiased clustering from bulk tissue RNA-seq?
... People use PCA for this as well, to eyeball how the samples group. Check out a deseq tutorial to see how to do that right. ...
written 5 days ago by swbarnes2 ♦ 7.5k
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Comment: C: Human DNA - Sequenced by Multiple Labs
... Do you have a favorite human cell line? ...
written 10 days ago by swbarnes2 ♦ 7.5k
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Comment: C: searching for specific RNA nucleotide sequences
... And grep the rev comp ...
written 12 days ago by swbarnes2 ♦ 7.5k
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104
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Answer: A: STAR error: EXITING because of FATAL ERROR in reads input: short read sequence l
... > I think that, for some reason, when I trim the data I am deleting one > of the pairs, them the aligner can not find the pairs of some reads > and I get the error. Specifically, I think what's happening is that you are trimming some reads to zero length. If your trimming steps are messin ...
written 13 days ago by swbarnes2 ♦ 7.5k
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Answer: C: Illumina index adapter trimming of FASTQ files using Cutadapt/TrimGalore
... 0.5%? You really don't have to worry about that if you don't want to. The N's are for the variable index region. You know what the index is, you can see it in the fastqc report. Why would you put N's in? ...
written 17 days ago by swbarnes2 ♦ 7.5k
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Comment: C: How to split fastq file containing Forward and Reverse reads to two files Forwar
... You can't identify what direction the read goes from the fastq. However, the bam file will tell you forward or reverse. ...
written 18 days ago by swbarnes2 ♦ 7.5k
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Comment: C: How to split fastq file containing Forward and Reverse reads to two files Forwar
... Do you really mean forward and reverse, and not read 1 and read and read 2? read1 and read2 can likely be split by their names. forward and reverse can only be determined after alignment. ...
written 18 days ago by swbarnes2 ♦ 7.5k
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Answer: A: Can I add the read counts to the re-sequenced read counts directly?
... If you sequenced the exact same library twice, and used the same gene counting pipelines, yes, you can just combine them. Barring a qc problem, running the library over again doesn't add any technical error. ...
written 21 days ago by swbarnes2 ♦ 7.5k

Latest awards to swbarnes2

Scholar 15 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 8 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 8 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Blast: Homology Or Similarity?
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
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: how to identify a sequencing sample's gender
Scholar 3 months ago, created an answer that has been accepted. For A: Problem with FPKM values
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
Scholar 4 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 5 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 6 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: Problem with FPKM values
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher 7 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 7 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 7 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 7 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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