User: Ranan Jyoti Sarma

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60
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Trusted
Location:
Mizoram University, India
Last seen:
5 days, 10 hours ago
Joined:
1 year, 11 months ago
Email:
r***********@gmail.com

Posts by Ranan Jyoti Sarma

<prev • 25 results • page 1 of 3 • next >
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Issue with Duplicates reads in Exom Data
... I have WES data and I have aligned it to hg19 using bwa mem. In BAM qc using qalimap, I am getting 26% duplicates reads in the BAM file. I used *Picard* with `REMOVE_DUPLICATES=true` option to remove the duplicates and I ran again *Qualimap* on the picard output where % of duplicates reads showing ...
duplicates alignment bam sequencing written 7 days ago by Ranan Jyoti Sarma60 • updated 7 days ago by i.sudbery7.7k
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Comment: C: Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
... Thanks for giving your time. Yes that is true. The name exist in the GTF file. Shall I use BioMart for adding gene names instead of AnnotationDb and org.Hs.eg.db? ...
written 17 days ago by Ranan Jyoti Sarma60
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Comment: C: Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
... Thank you so much. If I'm not wrong then org.Hs.eg.db package has no record for these IDs. The gene name exist in the GTF files when I checked it manually. Yes that's a great idea. I should Use gene_name instead of id while counting with htseq. ...
written 17 days ago by Ranan Jyoti Sarma60
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Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
... I have added gene name and Entrez ID in my DESeq2 result. The commands I have used are: res$hgnc_symbol <- convertIDs(gsub("\\..*","", row.names(res)), "ENSEMBL", "SYMBOL", org.Hs.eg.db) res$entrezgene <- convertIDs(gsub("\\..*","", row.names(res)), "ENSEMBL", "ENTREZID", org.Hs ...
ensembl deseq2 rna-seq written 18 days ago by Ranan Jyoti Sarma60 • updated 18 days ago by Kevin Blighe59k
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Comment: C: DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
... #Thanks, Problem is solved. ...
written 4 weeks ago by Ranan Jyoti Sarma60
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Comment: C: DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
... Yes. This is a normal RNA-seq. directory="~/Desktop/deseq2/" setwd(directory) sampleNames<- c("AN_d83", "AN_d85","AN_d86", "Tum_t83","Tum_t84","Tum_t85","Tum_t86") sampleCondition<- c("Adjacent Normal","Adjacent Normal","Adjacent Normal","Tumor","Tumor","Tumor" ...
written 4 weeks ago by Ranan Jyoti Sarma60
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DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
... I am using DESeq2 for differential gene expression. I have done alignment using STAR aligner and GRCh38 reference genome. I have generated count files using HTSeq. I have 3 controls and 4 cases and the size of each count file varies from 8 GB to 11 GB which makes to total 73 GB of data (7 Count fil ...
R deseq2 tool rna-seq written 4 weeks ago by Ranan Jyoti Sarma60
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Comment: A: Reduce label size in Volcano Plot
... Thank you for helping me out. ...
written 8 months ago by Ranan Jyoti Sarma60
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Clustering of Differentilly expressed gene of Cuffdiff
... Hi RNA-Seq Community. I have two lists of Upregulated and downregulated genes calculated by CuffDiff. But in visualization using R-CummRbund, clustering was missing on the heatmap. Is there any way to reconstruct the heatmap with clustering? ...
rna-seq genomics written 8 months ago by Ranan Jyoti Sarma60
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STAR-Fusion: Problem in interpreting
... Hi RNA-seq community Could anyone give me an idea about these two terms "JunctionReadCount" and "SpanningFragCount" of STAR-Fusion result? For some fusion, these numbers are very high (More than 100) and for some fusion, the numbers are extremely low (Less than 20). In this case, is there any t ...
rna-seq written 9 months ago by Ranan Jyoti Sarma60 • updated 9 months ago by lakhujanivijay5.0k

Latest awards to Ranan Jyoti Sarma

Scholar 12 months ago, created an answer that has been accepted. For A: very confused with GC bias

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