User: unique379

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unique37970
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Posts by unique379

<prev • 41 results • page 1 of 5 • next >
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Comment: C: htseq-counts output merge into one matrix ??
... No, you should use hts-seq on each replicates otherwise there is no meaning of replicates. By the way, you could use "featureCounts tool" for each bam at a time. Then, further you don't need to merge as its give you a matrix of count for each sample of bam. Hope this helps Good luck. ...
written 6 months ago by unique37970
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Problems with breakdancer (sv caller) output.
... Hi, I am trying to use results come from breakdancer and found multiple problems associated with the output vcf (converted using a python script by https://github.com/ALLBio/allbiotc2/blob/master/breakdancer/breakdancer2vcf.py). 1. Start and End Coordinates are not always correct (some END has smal ...
sv breakdancer next-gen svtyper delly written 6 months ago by unique37970
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Comment: C: Transform duplicate rows into columns.
... Thank you for introducing datamash, i never knew before. I have to install and check if its work for me. But thank you. ...
written 20 months ago by unique37970
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Comment: C: Transform duplicate rows into columns.
... Excellent Thank you. ...
written 20 months ago by unique37970
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Transform duplicate rows into columns.
... Hi all, I would like to make duplicate row lines as columns. So it would be easier to extract repetitive columns as comma separated format. These are transcript isoforms that means one gene has multiple transcript, which I want in one columns by comma separated. Input: 1_58420023_58420024 ...
R bash annotations rna-seq linux written 20 months ago by unique37970 • updated 20 months ago by cpad011211k
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Human and Mouse Benchmarking datasets for WGS, WES (variant callling) and RNASeq+differential analysis pipeline.
... Hello all, I am looking for Benchmarking datasets for WGS, WES and RNASeq analysis pipelines. Basically I need fastq, vcf file for WGS and WES and expression count for RNASeq that i can compare with my results. I found GIAB datasets but that contains different technologies which is i dont need, i j ...
dnaseq wes rna-seq wgs written 2.0 years ago by unique37970
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Need a piece of advice for microbiome data
... Dear folks, I am new to analyze for micro biome data. I am trying to use mothur for my analysis. I have MiSeq paired (fastq) microbiome data. After using contigs and summary.seqs command i need to screen the sequences from my reads. The sumary file look like this: mothur > summary.seqs(fast ...
microbiome miseq written 2.4 years ago by unique37970
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Designing of model.matrix for batch correction of Time Course data ?
... Dear folks, I would like to correct batch of my time course data but the problem is to design matrix for sva as input. So is there way to design matrix having **two groups (WT and KO) along with four time points (1 month, 3 months, 12 months and 22 months) including their replicates ??** > ...
sva ruvseq rna-seq written 3.1 years ago by unique37970 • updated 3.0 years ago by Biostar ♦♦ 20
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Comment: C: why my resultsNames(deseq) is not the same as model.matrix ?
... Thank you Ryan for your kind and efficient answer. I tried with full model then ran deseq wald and LRT test to see the differneces but got very surprising results for the same contrast. How it possible that, Wald Test gave me tags 0 at padj <0.05 while LRT test gave 345 tags at the same level of ...
written 3.1 years ago by unique37970
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why my resultsNames(deseq) is not the same as model.matrix ?
... Dear all, I have three question about RNASeq analysis of my data using DESeq2. Lets say i have 4 groups and wanna see DE for each combinations of the groups (**By specifying the contrast in results function of DESeq2**). So i used the default setting of DESeq considering intersect/base level (while ...
R sva deseq2 rna-seq written 3.1 years ago by unique37970 • updated 3.1 years ago by Devon Ryan91k

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