User: vivekbhr

gravatar for vivekbhr
vivekbhr540
Reputation:
540
Status:
Trusted
Location:
Germany
Website:
https://github.com/viv...
Twitter:
vivekbhr
Last seen:
11 months, 4 weeks ago
Joined:
4 years, 7 months ago
Email:
v***********@gmail.com

Posts by vivekbhr

<prev • 54 results • page 1 of 6 • next >
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Comment: C: RNA-seq HEK293T recent datasets
... I wouldn't expect much difference between the two ...
written 11 months ago by vivekbhr540
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Answer: A: hicAggregateContacts use with different HiC matrix format
... Hi. It depends on the format of your matrices. We provide [a tool][1] to convert between various HiC formats and HiCExplorer format. If you have your matrices in .cool format, or a homer-like format (all-to-all matrix), this would work. [1]: https://hicexplorer.readthedocs.io/en/latest/content/t ...
written 11 months ago by vivekbhr540
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Answer: A: RNA-seq HEK293T recent datasets
... We have both polyA plus and minus RNAseq on HEK293T cells, published recently : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85161 ...
written 2.3 years ago by vivekbhr540
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Answer: A: R reads q-score
... The [ShortRead][1] package in bioconductor is what you are looking for.. [1]: https://www.bioconductor.org/packages/release/bioc/html/ShortRead.html ...
written 2.7 years ago by vivekbhr540
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Tool: deepTools2 : User-friendly tools for exploring deep-sequencing data
... Although it was released last year, deepTools2 has not been formally introduced to the biostars community yet. **deepTools is a set of command line / galaxy tools for QC, normalization and visualization of sequencing data** deepTools addresses the challenge of handling the large amounts of data t ...
deeptools next-gen chip-seq tool rna-seq written 2.8 years ago by vivekbhr540 • updated 2.8 years ago by Devon Ryan93k
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Answer: A: The best way to correlate some genome wide signal to histone modification signal
... I can tell some [deepTools][1] solutions : a) genome-wide : Run multiBAMSummary of both files, followed by plotCorrelation. b) on some regions : Do peak calling from your ChIP-Seq data, take top peaks (bed) and do computematrix using histonemarks (bigWig), then plotHeatmap. [1]: http://deepto ...
written 2.8 years ago by vivekbhr540
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Comment: C: HISAT2 (graph index) alignment over InDels
... The InDels are 1 to 20 bp long, mostly on the shorter end of this range. I am simply trying to test whether graph index using known SNPs and InDels will give me better alignments in my data. It's a real RNA-seq data set from a mouse strain with known SNPs and InDels. I mapped initially using [anothe ...
written 2.9 years ago by vivekbhr540
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HISAT2 (graph index) alignment over InDels
... Hey Everyone I am mapping to mouse genome using HISAT2 and graph index (created using SNPs and InDels). The problem is that although HISAT2 finds alignments over the SNPs in the graph, it finds no alignments over InDels. I am using one chromsome, where I have around 288K SNPs and 36K InDels in th ...
alignment rna-seq written 2.9 years ago by vivekbhr540 • updated 2.9 years ago by Devon Ryan93k
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Comment: C: Deeptools: computeMatrix - Traceback
... What's your deeptools version? What happens if you try this with the latest version or develop version of deeptools? If the same command worked with same files before, but not now, them it much be the problem with one of the dependencies. Best is to install deeptools within the conda environment (ch ...
written 3.1 years ago by vivekbhr540
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Comment: C: Deeptools: computeMatrix - Traceback
... Numpy issue is possible, but could also be an issue with your summits file.. What happens if you try any other bed file instead of mysummit.summit ? ...
written 3.1 years ago by vivekbhr540

Latest awards to vivekbhr

Popular Question 16 months ago, created a question with more than 1,000 views. For HISAT2 (graph index) alignment over InDels
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Subsetting in R based on row name?
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Subsetting in R based on row name?
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Subsetting in R based on row name?
Student 2.9 years ago, asked a question with at least 3 up-votes. For HISAT2 (graph index) alignment over InDels
Supporter 3.1 years ago, voted at least 25 times.
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: Subsetting in R based on row name?
Scholar 3.7 years ago, created an answer that has been accepted. For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Scholar 3.9 years ago, created an answer that has been accepted. For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Scholar 4.3 years ago, created an answer that has been accepted. For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Scholar 4.3 years ago, created an answer that has been accepted. For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Scholar 4.6 years ago, created an answer that has been accepted. For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?

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