User: Ankit

gravatar for Ankit
Ankit140
Reputation:
140
Status:
Trusted
Location:
Europe
Last seen:
2 days, 6 hours ago
Joined:
2 years, 5 months ago
Email:
r**********@gmail.com
I am a bioinformatician working in the area of epigenetics

Posts by Ankit

<prev • 123 results • page 1 of 13 • next >
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Comment: C: sum counts in regions in bed format
... Hi, If I correctly understood your query, one way I can think of: Create you desired sliding window of genome (bedtools makeWindows). eg. 20 Kb may be. => File1.txt, Your bed file of CpGs => File2.txt Perform bedtools intersect File1.txt File2.txt. and concatenate the coordinates of CpGs ...
written 6 days ago by Ankit140
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RnBeads Greedycut command ???
... Hi everyone, Is this command from RnBeads R package is correct? # Remove probes and samples based on a greedy approach > rnb.set.filtered <- rnb.execute.greedycut(rnb.set.filtered)**$dataset** I did not get any output matrix. What I am missing I am nor sure if $dataset is the right ...
array greedycut methylation rnbeads written 24 days ago by Ankit140
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Comment: A: Coordinates for genomic features?
... Hi thanks Good suggestion. How about UCSC genome browser table https://genome.ucsc.edu/cgi-bin/hgTables Do you think is it correctly provide desired coordinates? I stiil dont know about promoter. So I thought to take 200 bp upstream of gene start. Does it make sense for approx promoter site ? ...
written 6 weeks ago by Ankit140
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Coordinates for genomic features?
... Hi Everyone, Can anyone help me how to get coordinates of the genome features for hg19? For example genes, Exon, intron, 5'utr and 3'utr , promoters. For genes and Exon I can get from gtf file. Right? The issue is with other features. Please suggest. Thank you ...
gene utr promoter exon intron written 6 weeks ago by Ankit140
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Comment: C: Batch correction methylation array datasets. any packages?
... Can you suggest a command specific for methylation data? ...
written 7 weeks ago by Ankit140
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Batch correction methylation array datasets. any packages?
... Dear all, Can anyone help me with batch correction for methylation array datasets? I have data from different labs. Some are 850K and other are 450K. I don't have raw idat files for some samples so I cannot use champ.runcombat function.. I thought to use Combat from svg package but I prefer ...
array methylation batch written 7 weeks ago by Ankit140
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Comment: C: RNA-seq and histone modifictaion
... Does public datasets contain same treatment in histone modifications of chip seq data or knockout, knockin, knockdown of your histone writer rna seq data? If yes directly correlate. If not try seeing the expression of histone writers gene in your Rnaseq data. . Eg. Setdb1 or any other writer of H3K ...
written 3 months ago by Ankit140
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Comment: C: Counting RNA-seq reads mapped to mRNAs (mouse)
... Use featurecounts or htseq-count. It needs a mouse gtf file too. You can download it from gencode or ucsc. ...
written 3 months ago by Ankit140
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Comment: C: draw consensus clustering heatmap
... Try pheatmap: https://davetang.org/muse/2018/05/15/making-a-heatmap-in-r-with-the-pheatmap-package/ ...
written 3 months ago by Ankit140
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Comment: C: p value from multiple columns using R??
... It seems it gives same p.values for all the regions? Why so? Something wrong I'm doing : My script: t.result <- apply(mymatrix, 1, function(x) t.test(mymatrix[,24:35],mymatrix[,36:39], paired=FALSE)$p.value) I applied this on large matrix 24:35 are all controls , 36:39 are all cases. Is ...
written 3 months ago by Ankit140

Latest awards to Ankit

Popular Question 10 weeks ago, created a question with more than 1,000 views. For No mismatch allowed setting in Bowtie2 (-N 0 does not help)
Centurion 4 months ago, created 100 posts.
Popular Question 7 months ago, created a question with more than 1,000 views. For How to extract uniquely mapped reads in Bowtie2
Popular Question 7 months ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq
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Popular Question 13 months ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq
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