User: vivekbhr
vivekbhr • 540
- Reputation:
- 540
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- 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
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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
vivekbhr • 540
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... 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
vivekbhr • 540
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... 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
vivekbhr • 540
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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
vivekbhr • 540
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... 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 ...
written 2.8 years ago by
vivekbhr • 540
• updated
2.8 years ago by
Devon Ryan ♦ 93k
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... 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
vivekbhr • 540
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... 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
vivekbhr • 540
4
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5 follow
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... 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 ...
written 2.9 years ago by
vivekbhr • 540
• updated
2.9 years ago by
Devon Ryan ♦ 93k
0
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2
answers
2.9k
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2
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... 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
vivekbhr • 540
0
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2
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2.9k
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2
answers
... 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
vivekbhr • 540
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?
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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
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3.1 years ago,
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3.6 years ago,
created a post with more than 5 votes.
For A: Subsetting in R based on row name?
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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,
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For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Scholar
3.9 years ago,
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For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Teacher
3.9 years ago,
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For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Scholar
4.3 years ago,
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For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Teacher
4.3 years ago,
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For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Scholar
4.3 years ago,
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For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Scholar
4.6 years ago,
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For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
Teacher
4.6 years ago,
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For A: Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
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