User: vivekbhr

gravatar for vivekbhr
vivekbhr630
Reputation:
630
Status:
Trusted
Location:
Germany
Website:
https://github.com/viv...
Twitter:
vivekbhr
Last seen:
6 months, 3 weeks ago
Joined:
5 years, 10 months ago
Email:
v***********@gmail.com

Posts by vivekbhr

<prev • 54 results • page 2 of 6 • next >
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Answer: A: How do I find unmapped reads in my sam file?
... Use samtools. Just do `samtools view -f 4 ` .. You can extract all kinds of reads by specifying the flag No. after `samtools -f` . Get the relevant flags [here](https://broadinstitute.github.io/picard/explain-flags.html) ...
written 4.4 years ago by vivekbhr630
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Comment: C: number of grouping affect log2 fold change in DESeq2 analysis?
... How come no differentially expressed gene has fdr below 0.03? I guess you have some kind of filtering going on .. ...
written 4.5 years ago by vivekbhr630
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Answer: A: Extracting ids of a cluster in heatmap
... You can create your own dendrograms, using the `hclust` function, give this output to pheatmap to make heatmap (`cluster_rows` option ) . Then cut the clusters of your dendrogram using the `cutree` function in R to get a vector that tells you which entry belongs to which cluster. ...
written 4.5 years ago by vivekbhr630
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Comment: C: Deeptools: computeMatrix - Traceback
... How does the traceback look this time? ...
written 4.5 years ago by vivekbhr630
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Comment: C: Deeptools: computeMatrix - Traceback
... Hi Can you post the command the you are using, and the output error, but this time using only single processor (-p 1) ? This will give more idea about the error. ...
written 4.5 years ago by vivekbhr630
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Comment: C: circRNA- seq normalization
... If you are using edgeR/DEseq the library size normalization should be enough. ...
written 4.5 years ago by vivekbhr630
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Answer: C: DESeq2 design and interaction terms
... So you're interested in condition B vs A, taking care of interaction between genotype II vs I (KO over WT) ? Then it should be `genotypeII.conditionB` result. ...
written 4.5 years ago by vivekbhr630
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Comment: C: Bioconductor as a source for the dependencies of an R package?
... @Vivian you need to add a term to biocViews. Eg : `biocViews : rnaseq` ...
written 4.6 years ago by vivekbhr630
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Answer: A: Subsetting in R based on row name?
... Hi. . Just replace your **==** with **%in%** ...
written 4.9 years ago by vivekbhr630
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Answer: A: Annotate peaks based on Histone Mark
... You can cluster your peaks using the histone marks signals in the region and visualize them using **deepTools2**... Have a look at computematrix and plotHeatmap/plotProfile tools.. (https://deeptools.readthedocs.org) ...
written 4.9 years ago by vivekbhr630

Latest awards to vivekbhr

Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Subsetting in R based on row name?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For deepTools2 : User-friendly tools for exploring deep-sequencing data
Scholar 2.2 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 2.2 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?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For HISAT2 (graph index) alignment over InDels
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Subsetting in R based on row name?
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Subsetting in R based on row name?
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Subsetting in R based on row name?
Student 4.1 years ago, asked a question with at least 3 up-votes. For HISAT2 (graph index) alignment over InDels
Supporter 4.3 years ago, voted at least 25 times.
Appreciated 4.8 years ago, created a post with more than 5 votes. For A: Subsetting in R based on row name?
Scholar 4.9 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 4.9 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?
Teacher 5.2 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 5.2 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 5.2 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 5.5 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 5.5 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 5.5 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 5.8 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 5.8 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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