User: Ankit

gravatar for Ankit
Ankit170
Reputation:
170
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Trusted
Location:
Europe
Last seen:
7 hours ago
Joined:
2 years, 9 months ago
Email:
r**********@gmail.com
I am a bioinformatician working in the area of epigenetics

Posts by Ankit

<prev • 130 results • page 1 of 13 • next >
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Comment: C: Prop.test for multiple rows/or full matrix and get p.values ?
... The concept is to see allelic differences. Basically to get statistically significant genes expression between two alleles i.e allele1 and allele2. For replicate 1, $n = sample1.sum $x = sample1.allele1 For replicate 2, $n = sample2.sum $x = sample2.allele1 ...
written 9 weeks ago by Ankit170
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Comment: C: Prop.test for multiple rows/or full matrix and get p.values ?
... Here is the normalized count matrix: Gene sample1.allele1 sample2.allele1 sample1.allele2 sample2.allele2 sample1.sum sample2.sum Gene1 603.0048247277 869.4788427557 546.7243744198 791.9740688625 1149.7291991476 1661.4529116183 Gene2 27.5659348447 41.8703950917 39.05174103 19.5989083 ...
written 9 weeks ago by Ankit170
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Comment: C: Prop.test for multiple rows/or full matrix and get p.values ?
... for now I tried to use this, if it make sense myout.p <- data.frame(capture.output(for (i in seq_along(myout)){ cat(myout[[i]]$p.value, "\n") })) ...
written 9 weeks ago by Ankit170
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Prop.test for multiple rows/or full matrix and get p.values ?
... Hi everyone, I have a matrix of gene expression. I want to apply prop.test function in r for each row and obtain p.values only. How to to do that in R ? My attempts are as follows: 1. myout <- purrr::pmap(countmatrix,~{prop.test(x = countmatrix$x, n = countmatrix$n, correct = "FALSE")}) ...
matrix prop.test statistics written 9 weeks ago by Ankit170
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Quantify Isoforms in RNA-Seq data
... Hi everyone, I know this question has been asked multiple times in other [posts][1], but I am still not clear. I want to quantify counts for each isoforms. I am not sure how it will be possible specially for overlapping transcripts. I think featurecounts is not good for isoform quantitation. I n ...
isoforms rna-seq written 12 weeks ago by Ankit170 • updated 12 weeks ago by kristoffer.vittingseerup3.5k
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Comment: C: Tools to call Large indels/structural variations in whole genome BAM data of mo
... Thanks for help. Any other alternative software. I could not understand the package well. ...
written 3 months ago by Ankit170
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Tools to call Large indels/structural variations in whole genome BAM data of mouse strain?
... Hi everyone, I would like to know if there are tools to call large indels/structural variations in data of mouse strain. I have bam files obtained online from ftp://ftp-mouse.sanger.ac.uk/REL-1905-BAM/. The data was aligned to GRCm38. For reference genome I have fasta file. I specifically want ...
indels structural variations whole genome mouse written 3 months ago by Ankit170 • updated 3 months ago by d-cameron2.3k
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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 4 months ago by Ankit170
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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 5 months ago by Ankit170
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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 5 months ago by Ankit170

Latest awards to Ankit

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Normalization of allele specific counts in RNA-seq
Popular Question 6 months ago, created a question with more than 1,000 views. For No mismatch allowed setting in Bowtie2 (-N 0 does not help)
Centurion 8 months ago, created 100 posts.
Popular Question 11 months ago, created a question with more than 1,000 views. For How to extract uniquely mapped reads in Bowtie2
Popular Question 11 months ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq
Supporter 13 months ago, voted at least 25 times.
Popular Question 17 months ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq
Popular Question 22 months ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq

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