User: Amar

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Amar620
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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 13 days ago by Amar620
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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 13 days ago by Amar620
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Comment: C: de novo transcriptome annotation steps
... What organism are you working with? ...
written 14 days ago by Amar620
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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 14 days ago by Amar620
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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 14 days ago by Amar620
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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 14 days ago by Amar620
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Comment: C: Question: Viromescan tool for metagenomics analysis:Failed to find bmfilter
... No idea sorry! Try contacting the developers. ...
written 14 days ago by Amar620
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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 14 days ago by Amar620
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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 15 days ago by Amar620
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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 15 days ago by Amar620

Latest awards to Amar

Teacher 16 days 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 18 days 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 18 days 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 weeks ago, created 100 posts.
Teacher 6 weeks 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 6 weeks ago, voted more than 100 times.
Scholar 6 weeks ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 6 weeks ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 6 weeks ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Scholar 6 weeks ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Teacher 6 weeks 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 6 weeks ago, created an answer that has been accepted. For A: Parsing an ExpressionSet for all SRA addresses
Supporter 16 months ago, voted at least 25 times.

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