User: Vikas Bansal

gravatar for Vikas Bansal
Vikas Bansal2.3k
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Location:
Berlin, Germany
Website:
http://www.molgen.mpg.de/
Last seen:
5 days, 11 hours ago
Joined:
5 years, 9 months ago
Email:
v***********@yahoo.co.in

PhD student (Bioinformatics)

Posts by Vikas Bansal

<prev • 271 results • page 1 of 28 • next >
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Comment: C: Calculate Percent Spliced In (PSI)
... Thanks. I think I found a bug and I will post it on github. Just one thing- Did you publish jvarkit? I found it quite fast. Although I never use java, I found it easy to use. ...
written 3.5 years ago by Vikas Bansal2.3k
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Comment: C: Calculate Percent Spliced In (PSI)
... Here is the link for the BAM (subset) file - https://www.dropbox.com/s/k2ibkw81t4hexq8/onlymyh7.bam and gtf I downloaded from here - http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=378435437_BVHytx2vRGH3XVmRsp39JG5acTeD&clade=mammal&org=Mouse&db=mm9&hgta_group=genes&hgta_track=ref ...
written 3.5 years ago by Vikas Bansal2.3k
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Comment: C: Calculate Percent Spliced In (PSI)
... Finally, I got the output file. But the columns - "exon.count_prev_and_next", "exon.count_prev_and_curr" "exon.count_curr_and_next" are all 0. I think it is not able to calculate junction reads. ...
written 3.5 years ago by Vikas Bansal2.3k
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Comment: C: Calculate Percent Spliced In (PSI)
... Thanks. Now build is fine. But when I do "ant biostar103303" or "ant Biostar103303" or "ant Biostar103303.java" , it says Buildfile: /project/specht/tools/jvarkit/htsjdk/build.xml BUILD FAILED Target "biostar103303" does not exist in the project "htsjdk". Total time: 0 seconds   ...
written 3.5 years ago by Vikas Bansal2.3k
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Comment: C: Calculate Percent Spliced In (PSI)
... Thanks a lot for the reply. Its amazing that you included it in jvarkit so quickly. I am trying to install jvarkit but it is not working. Below are my commands (in bold)-   java -version java version "1.8.0_05" ant -version Apache Ant(TM) version 1.9.4 compiled on April 29 2014 git clone "https: ...
written 3.5 years ago by Vikas Bansal2.3k
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Comment: C: Calculate Percent Spliced In (PSI)
... Thanks for the reply. I read about MISO but it says  Two general kinds of analyses are possible: Estimate expression level of exons (“exon-centric” analysis) or, Estimate expression level of whole transcripts (“isoform-centric” analysis) I think it include the reads mapped on exons but I am i ...
written 3.5 years ago by Vikas Bansal2.3k
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Calculate Percent Spliced In (PSI)
... Dear all, I was wondering if there is any tool to calculate PSI from the BAM files. Basically what I want is-   I have gtf file with all the exons and I want to calculate for each exon (lets take exon filled with grey for example) how many reads mapped to junction of that exon (a and b in figur ...
splicing rna-seq written 3.5 years ago by Vikas Bansal2.3k • updated 3.5 years ago by Pierre Lindenbaum102k
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Answer: A: Barplot With Standard Deviation Simple Data
... Not a specific answer but I was just reading these news articles from nature methods yesterday - Points of Significance: Visualizing samples with box plots and Points of View: Bar charts and box plots Hope this helps. ...
written 3.9 years ago by Vikas Bansal2.3k
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Forum: Outlier-Based Cnv Calling Method
... We recently published a paper 'Outlier-Based Identification of Copy Number Variations Using Targeted Resequencing in a Small Cohort of Patients with Tetralogy of Fallot'. I think it will be interesting for someone working on copy number variations. Advantages- 1. Calling CNVs from small cohort. 2. D ...
forum cnv written 3.9 years ago by Vikas Bansal2.3k
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Answer: A: How To Compute The Significance Of The Overlap Of The Size Of The Intersection O
... For a quick solution, look at this page. A web based CGI scripts that computes the Statistical significance of the overlap between two groups of genes via the hypergeometric distribution/ ...
written 4.3 years ago by Vikas Bansal2.3k • updated 4.3 years ago by Istvan Albert ♦♦ 75k

Latest awards to Vikas Bansal

Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Simple Question: What Is "Large" For Bwa?
Great Question 3 months ago, created a question with more than 5,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For Cnv Visualisation Tools
Great Question 8 months ago, created a question with more than 5,000 views. For Cnv Visualisation Tools
Great Question 8 months ago, created a question with more than 5,000 views. For Cnv Visualisation Tools
Epic Question 8 months ago, created a question with more than 10,000 views. For Output Of Chip-Seq Data Analysis Using Macs
Popular Question 11 months ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Great Question 13 months ago, created a question with more than 5,000 views. For Mapping Large Fastq Files With Bwa
Great Question 14 months ago, created a question with more than 5,000 views. For Calculate Percent Spliced In (PSI)
Great Question 15 months ago, created a question with more than 5,000 views. For Mapping Large Fastq Files With Bwa
Popular Question 16 months ago, created a question with more than 1,000 views. For Histone Modification Database For Positive And Negative
Student 16 months ago, asked a question with at least 3 up-votes. For Identify Summit Positions From Bed File
Popular Question 16 months ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 19 months ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 19 months ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 21 months ago, created a question with more than 1,000 views. For Peak Calling In Encode Project
Popular Question 23 months ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 23 months ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 24 months ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Peak Calling In Encode Project
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Histone Modification Database For Positive And Negative
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Cnv Visualisation Tools
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: How Can I Include One Bed File In Another Bed File ?
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Simple Question: What Is "Large" For Bwa?

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