User: Vivek.b

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Vivek.b40
Reputation:
40
Status:
New User
Location:
Germany
Website:
https://github.com/viv...
Twitter:
vivekbhr
Last seen:
15 hours ago
Joined:
2 years, 10 months ago
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Posts by Vivek.b

<prev • 34 results • page 1 of 4 • next >
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Comment: C: bplapply with ShortRead functions
... Thanks Martin. I think the issue was the second one you mentioned. Today I killed some processes on my computer and freed a few GBs of memory, and the function is now working. So it needed more memory when executed multi-core than on single core. Weird coincidence for me, yesterday I tried on our Rs ...
written 7 days ago by Vivek.b40
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bplapply with ShortRead functions
... Hey everyone I am facing an issue with using ShortRead functions with bplapply. I am trying to demultiplex a fastq file. Following is an example function, which does nothing but creates multiple paired-end fastq files, all containing same reads : demultiplex_fastq <- function(fastq_R1, fastq_R ...
shortread biocparallel written 8 days ago by Vivek.b40 • updated 8 days ago by Martin Morgan ♦♦ 21k
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Comment: C: csaw : effect of library size on filtering of uninteresting windows
... Got it.. Thanks Aaron.. I want you to keep doing your great job :) ...
written 11 months ago by Vivek.b40
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csaw : effect of library size on filtering of uninteresting windows
... Hi there, I am trying the csaw package to filter the background from my data using the "local enrichment" method. I first tested in a dataset with low input material (resulting in low library sizes) and find that the method works nicely, when I keep all regions with 2-fold enrichment over the local ...
csaw written 11 months ago by Vivek.b40 • updated 11 months ago by Aaron Lun18k
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Rsamtools filterBam question
... Hi Everyone I have two questions related to Rsamtools : 1. I am trying to filter my bam file by scanning the genome in 1kb bins, and removing reads that match certain criteria. But I will have to bin the genome chromosome by chromosome and run the filtering per chromosome.. I created the followin ...
rsamtools written 18 months ago by Vivek.b40
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Comment: C: diffHiC differential HiC analysis starting from Ginteractions object
... Thanks Aaron. This works.. ...
written 18 months ago by Vivek.b40
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Comment: C: diffHiC differential HiC analysis starting from Ginteractions object
... Hi Aaron Thanks for the reply. Using restriction frag size produced different bin sizes (since sometime i get a cut, sometimes not. plus they are different cell lines). But I now overcome this by using fixed bin size to create the matrix (not restriction frag length).  I can overcome #3 since I ha ...
written 18 months ago by Vivek.b40
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diffHiC differential HiC analysis starting from Ginteractions object
... Hi  I would like to use difHiC to get differential domains using two different cell lines. I have converted my normalized matrix for each of them into GInteraction objects.   ``` $s2 GInteractions object with 6398123 interactions and 1 metadata column: seqnames1 ranges1 ...
diffhic interactionset written 18 months ago by Vivek.b40
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Answer: A: CAGEr : problem while filtering the bamFile
... I solved the problem today. Although it was a silly thing but was hard to catch. The problem was that I mapped my data using ENSEMBL annotation, and had no "chr" in my seqnames. Since the getCTSS methods uses this :  reads.GRanges <- reads.GRanges[seqnames(reads.GRanges) %in% seqnames(genome)] ...
written 2.0 years ago by Vivek.b40
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CAGEr : problem while filtering the bamFile
... Dear CAGEr team I have been trying to run CAGEr on my test dataset and having problem in reading in the BAM files to make CAGEset object. > input = list.files("test",pattern = "test-.*sorted.bam$",full.names = TRUE) > mycage <- new("CAGEset", genomeName = "BSgenome.Dmelanogaster.UCSC.dm6 ...
cager cage written 2.0 years ago by Vivek.b40

Latest awards to Vivek.b

Great Question 13 months ago, created a question with more than 5,000 views. For RDAVIDWebService Error 301: Moved Permanently
Supporter 2.1 years ago, voted at least 25 times.
Popular Question 2.4 years ago, created a question with more than 1,000 views. For RDAVIDWebService Error 301: Moved Permanently

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