User: Vikas Bansal

gravatar for Vikas Bansal
Vikas Bansal2.3k
Reputation:
2,310
Status:
Trusted
Location:
Berlin, Germany
Website:
http://www.molgen.mpg.de/
Last seen:
3 weeks, 3 days ago
Joined:
6 years, 10 months ago
Email:
v***********@yahoo.co.in

PhD student (Bioinformatics)

Posts by Vikas Bansal

<prev • 271 results • page 1 of 28 • next >
0
votes
1
answer
11k
views
1
answers
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 4.5 years ago by Vikas Bansal2.3k
0
votes
1
answer
11k
views
1
answers
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 4.5 years ago by Vikas Bansal2.3k
0
votes
1
answer
11k
views
1
answers
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 4.5 years ago by Vikas Bansal2.3k
0
votes
1
answer
11k
views
1
answers
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 4.5 years ago by Vikas Bansal2.3k
0
votes
1
answer
11k
views
1
answers
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 4.5 years ago by Vikas Bansal2.3k
0
votes
1
answer
11k
views
1
answers
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 4.5 years ago by Vikas Bansal2.3k
10
votes
1
answer
11k
views
7 follow
1
answer
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 4.5 years ago by Vikas Bansal2.3k • updated 4.5 years ago by Pierre Lindenbaum115k
3
votes
2
answers
2.2k
views
2
answers
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 4.9 years ago by Vikas Bansal2.3k
3
votes
0
answers
1.2k
views
0
answers
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 4.9 years ago by Vikas Bansal2.3k
2
votes
2
answers
9.9k
views
2
answers
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 5.3 years ago by Vikas Bansal2.3k • updated 5.3 years ago by Istvan Albert ♦♦ 78k

Latest awards to Vikas Bansal

Popular Question 3 months ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Epic Question 5 months ago, created a question with more than 10,000 views. For Output Of Chip-Seq Data Analysis Using Macs
Student 5 months ago, asked a question with at least 3 up-votes. For Identify Summit Positions From Bed File
Popular Question 9 months ago, created a question with more than 1,000 views. For Repetitive Regions In Hg18
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Simple Question: What Is "Large" For Bwa?
Great Question 15 months ago, created a question with more than 5,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Good Question 20 months ago, asked a question that was upvoted at least 5 times. For Cnv Visualisation Tools
Great Question 20 months ago, created a question with more than 5,000 views. For Cnv Visualisation Tools
Great Question 20 months ago, created a question with more than 5,000 views. For Cnv Visualisation Tools
Epic Question 21 months ago, created a question with more than 10,000 views. For Output Of Chip-Seq Data Analysis Using Macs
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
Great Question 2.1 years ago, created a question with more than 5,000 views. For Mapping Large Fastq Files With Bwa
Great Question 2.2 years ago, created a question with more than 5,000 views. For Calculate Percent Spliced In (PSI)
Great Question 2.3 years ago, created a question with more than 5,000 views. For Mapping Large Fastq Files With Bwa
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Histone Modification Database For Positive And Negative
Student 2.4 years ago, asked a question with at least 3 up-votes. For Identify Summit Positions From Bed File
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Peak Calling In Encode Project
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Fpkm Comparison Using T-Test Or Mann-Whitney U Test
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Peak Calling In Encode Project
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Histone Modification Database For Positive And Negative

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 860 users visited in the last hour