User: Amar

gravatar for Amar
Amar640
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Posts by Amar

<prev • 172 results • page 1 of 18 • next >
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Comment: C: logFC in topTable problem- almost identical to average expression
... That is weird. Maybe it's because your contrast are essentially the same? Early vs Late is the same as Late vs Early (only the logFC direction will change). I think you don't need the contrast at all because your design is simple (AvsB). ...
written 4 months ago by Amar640
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Comment: C: de novo transcriptome annotation steps
... Here's a really good protocol from a paper: https://www.protocols.io/view/de-novo-transcriptome-assembly-workflow-ghebt3e/abstract One of the things I love is the detail and the multi-tool approach. I hope it helps! ...
written 4 months ago by Amar640
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Comment: C: de novo transcriptome annotation steps
... What organism are you working with? ...
written 4 months ago by Amar640
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Comment: C: FeatureCounts for miRNAseq
... Thanks for the correction. What's the difference between micro and small RNA? or are they different terms for the same thing. ...
written 4 months ago by Amar640
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Comment: C: FeatureCounts for miRNAseq
... Im guessing your question is, why do you have ~58m reads aligned but on ~26k reads assign to features? The answer is probably because your gff file combined with your sequencing strategy. Try using a more "generic" gff file to see what's been sequenced/aligned. But another issue i see is that you ...
written 4 months ago by Amar640
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Comment: C: Invalid covariate name
... Do you get the same error on the unfiltered `bg` data set? btw this is the code that's generating the error: colind = which(names(pData) == covariate) if(length(colind) == 0) stop("invalid covariate name") It's checking if the covariate specified exists in your dataframe. For whate ...
written 4 months ago by Amar640
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Comment: C: Question: Viromescan tool for metagenomics analysis:Failed to find bmfilter
... No idea sorry! Try contacting the developers. ...
written 4 months ago by Amar640
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Comment: C: Should normalization of expression data be performed over the entire dataset or
... What version of R are you using? Make sure it's 64bit. Also use `fread` from `data.table` to read in your file. ...
written 4 months ago by Amar640
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Comment: C: Size of Output BAM file bigger than the SUM Size of Input files after merging wi
... Try sorting `File_1p2.bam`. That should reduce the size. ...
written 4 months ago by Amar640
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Comment: C: Question: Viromescan tool for metagenomics analysis:Failed to find bmfilter
... I think you haven't performed the installation correctly. `bmfilter` is missing from this location: `mnt/data5/sunzheng/tools/viromescan/tools/bmfilter` and the instructions say: > If you downloaded Bmtools, you will have to move bmtagger.sh, bmfilter, bmtool, extract_fullseq and srprism script ...
written 4 months ago by Amar640

Latest awards to Amar

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to perform local realignment around indels without a known vcf file of indel
Scholar 4 months ago, created an answer that has been accepted. For A: How to perform local realignment around indels without a known vcf file of indel
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to perform local realignment around indels without a known vcf file of indel
Centurion 5 months ago, created 100 posts.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to perform local realignment around indels without a known vcf file of indel
Voter 5 months ago, voted more than 100 times.
Scholar 5 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 5 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 5 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 5 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to perform local realignment around indels without a known vcf file of indel
Scholar 5 months ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Supporter 19 months ago, voted at least 25 times.

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