User: Sumit Paliwal

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Posts by Sumit Paliwal

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Cluster samples based on expression of a subset of genes
... Hi Karl, Thanks for the info. The issue in my case is that I want to define sample groups based on expression of a subset of genes and then do a differential expression (DE) analysis. I do not know if I can in some way use raw/normalized counts of these subset of genes to categorize samples and subs ...
written 9 months ago by Sumit Paliwal20
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Comment: C: Cluster samples based on expression of a subset of genes
... Hi kristoffer, I have HTSeq counts from some TCGA cancer samples. ...
written 9 months ago by Sumit Paliwal20
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Cluster samples based on expression of a subset of genes
... Hi All, I have RNA-Seq data on some cancer samples. I would like to cluster these samples based on the expression of a defined subset of genes. Subsequently, I want to select those samples that are with the highest and lowest expression of this gene subset. I am not sure how to do it. Any suggestion ...
cluster rna-seq written 9 months ago by Sumit Paliwal20 • updated 8 months ago by kristoffer.vittingseerup2.2k
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Comparing Human and Mouse expression data
... Hi All, I have RNA-Seq data from knockout mice for a gene X and have identified differentially expressed genes (DEGs) compared to wild type mice. Now I want to explore what is the status of these genes in the GteX dataset. Basically, I want to look if in the GTex dataset, in the same tissue, if thes ...
rna-seq gtex written 10 months ago by Sumit Paliwal20
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Cuffmerge on all samples or only on those that I need to include in differential expression analysis?
... Hi, I have performed RNA-seq on samples from two different conditions (each with atleast two or three replicates). I have aligned the samples using tophat and now wish to perform differential expression analysis using Cufflinks. I have a query about cuffmerge. I suspect a replicate sample from one c ...
cufflinks cuffmerge rna-seq written 23 months ago by Sumit Paliwal20 • updated 23 months ago by Kevin Blighe47k
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Comment: C: No change in number of reads and quality after removing rRNA contamination using
... Here is the image of the FastQC Basic Statistics prior to removal of rRNA reads: ![FastQC-before][1] SeqMonk RNASeq QC report suggesting rRNA contamination: ![SeqMonk RNASeq QC][2] I used the following command to remove rRNA reads: while read i do /home/svsgrc/Sumit/RNASeq/sortmer ...
written 2.2 years ago by Sumit Paliwal20
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Answer: A: How to remove rRNA, bacterial RNA and polyA contamination from RNA-seq data(fast
... I don't know if you have done it but you can use fastq_screen to check for cross-species or other (e.g adapters) contaminations. You can also load your aligned SAM/BAM files in SeqMonk for an RNASeq QC report. SeqMonk is GUI based and hence user friendly. Thereafter as suggested above you can prob ...
written 2.2 years ago by Sumit Paliwal20
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Comment: C: No change in number of reads and quality after removing rRNA contamination using
... In my samples it ranges from 5%-25%. I think it is a significant amount. ...
written 2.2 years ago by Sumit Paliwal20
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Comment: C: No change in number of reads and quality after removing rRNA contamination using
... rRNA contamination in my samples ranges from 5%-25%. With this level of contamination, I should see a difference in number of reads before and after processing files with sortmerna. My concern is that I do not see any difference, although I find that there are a significant number of reads that mat ...
written 2.2 years ago by Sumit Paliwal20
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No change in number of reads and quality after removing rRNA contamination using sortmerna
... Hi Everyone, I have done RNA-seq (75 bp paired-end; 50 million reads per sample) on some samples to assess differential expression. Initial FastQC report showed some sequence duplications issue. Despite that, I did the alignment and imported the resulting BAM files in Seqmonk for further analysis. ...
seqmonk sortmerna rna-seq fastqc written 2.2 years ago by Sumit Paliwal20

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Popular Question 23 months ago, created a question with more than 1,000 views. For No differentially expressed genes using DESeq2

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