Moderator: swbarnes2

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swbarnes27.2k
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Posts by swbarnes2

<prev • 870 results • page 2 of 87 • next >
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Comment: C: Alignment using BWA tool
... Are you sure trimming one fastq and not the other is what you want? ...
written 18 days ago by swbarnes27.2k
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Comment: C: Can anyone suggest me the recent and best pipeline for RNA-Seq data analysis
... You should figure that people answering will not want to put in more than half the effort answering that you demonstrated you put in already. How much effort do you think you've demonstrated so far? ...
written 24 days ago by swbarnes27.2k
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Comment: C: Paired end data with R1 demultiplexed but not R2
... What application are you doing? Are sequencing services really so lazy that they won't demultiplex samples? What on earth is gained by pushing that off to the end user? ...
written 24 days ago by swbarnes27.2k
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Comment: C: Extract all BAM reads that intersect a given region using the BAI index
... It's a better use of your time to not reinvent the wheel, but to learn how to use the tools that everyone else already uses and understands. It also makes it easier for people to replicate what you did if you use common tools. ...
written 25 days ago by swbarnes27.2k
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Answer: A: Extract all BAM reads that intersect a given region using the BAI index
... Why can't you use samtools? ...
written 25 days ago by swbarnes27.2k
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Answer: A: converting RF strand-specific mRNA sequencing data to FR stand-specific
... Don't do that. Just process each sample properly. ...
written 26 days ago by swbarnes27.2k
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Answer: A: Bulk RNA-Seq pipeline suggestion incorporating UMIs
... Have you looked at umi-tools? https://github.com/CGATOxford/UMI-tools ...
written 28 days ago by swbarnes27.2k
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Comment: C: Error when running cellranger mkref single nuclei RNA-Seq
... If you scroll down, you'll see that for single nuclei applications, you need to do the tweaks the OP described to the gtf before mkref, so the OP does have to make their own index locally. (Looks like you relabel 'transcripts' as 'exons' so it won't expect introns to be omitted) ...
written 4 weeks ago by swbarnes27.2k
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Comment: C: What is the Variance means in PCA plot ?
... Your p-values are meaningless, and your fold changes might be nonsense, because you have no replicates. ...
written 5 weeks ago by swbarnes27.2k
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Answer: A: What is the Variance means in PCA plot ?
... > i had some error for analyzing them and the results were wrong. So i > turned them into single ends, and i got acceptable results. That was a really really horrible idea. You have no replicates, so you are lying to your software pretending you have replicates. When you lie to software, y ...
written 5 weeks ago by swbarnes27.2k

Latest awards to swbarnes2

Teacher 14 hours ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Commentator 13 days ago, created a comment with at least 3 up-votes. For C: how to identify a sequencing sample's gender
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
Scholar 9 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 11 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 11 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
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 4 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 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 4 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 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 4 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 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
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
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Exon-Seq Mutation Detection
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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