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User: Anil Kesarwani

gravatar for Anil Kesarwani
Reputation:
90
Status:
Trusted
Location:
United States
Last seen:
3 years, 6 months ago
Joined:
6 years, 6 months ago
Email:
k*************@gmail.com

Posts by Anil Kesarwani

<prev • 27 results • page 2 of 3 • next >
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Differential quantification of splice junction
... Hi, From TopHat 2 alignment, I have obtained outputs containg splice junctions and the corresponding read counts. I am interested in calculating differential splice junction usage between wild type and mutant samples. In a recent publication (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358997/ ), ...
dexseq rna-seq written 5.7 years ago by Anil Kesarwani • 90 • updated 5.7 years ago by SES ♦ 8.4k
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How to count novel and known splice junction reads from BAM
... Hi, I have BAM file from TopHat 2 alignment with RefSeq genes annotation. Is there any way to count separately the exon junction reads comming from RefSeq transcripts and novel junctions (not from RefSeq). Could somebody help me out. ...
tool rna-seq written 5.7 years ago by Anil Kesarwani • 90 • updated 5.7 years ago by Jordan • 1.2k
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Tool: rMATS: quantification of differential splicing
... I have been using rMATS for quite some times, and I found it one of the best tools for splicing studies. However, I don't understand how rMATS handles following situation: How differential splicing between two samples is calculated for those cases where the alternative splicing has read supports on ...
tool rna-seq written 5.7 years ago by Anil Kesarwani • 90
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Answer: A: Can I Pre-Build The Shared Transcriptome Index For A Series Of Tophat Runs?
... Create the transcritome index for the first tophat run. For the next tophat run, the program will use the same index. ...
written 6.1 years ago by Anil Kesarwani • 90
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How does MISO quantify genes with single isoform
... Hi, I am using MISO to quantify the expression level of individual isoforms annotated in ENSEMBL GRCh37.65. I want to highlight that I am NOT quantifying only the region covering alternative splicing event, rather the full length isoform. The input GFF file contains annotation of genes encoding sin ...
tool rna-seq written 6.2 years ago by Anil Kesarwani • 90 • updated 6.2 years ago by Istvan Albert ♦♦ 86k
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Quantitative anlysis of alternative splicing events
... Hi, I have aligned paired-end reads to hg19 ref. genome using STAR. Before aligning, the reads were preprocessed to remove adapter sequences using Trimmomatic, and thus the reads aligned had varying lengths ranging from minimum 25 to maximum 76 nt. I want to extract different types of AS event, fo ...
tool rna-seq written 6.3 years ago by Anil Kesarwani • 90 • updated 6.3 years ago by Sean Davis ♦ 26k
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Comment: C: How to run MISO with ENSEMBL GTF if reads were aligned against UCSC genome
... Thanks for the explanation. I am using UCSC hg19, and ENSEMBL genome release 37 ...
written 6.4 years ago by Anil Kesarwani • 90
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Comment: C: How to run MISO with ENSEMBL GTF if reads were aligned against UCSC genome
... Thanks. For that, I just changed the chromosome names in ENSEMBL file as per the UCSC convention. However, its in MISO homepage, where it has been suggested to re-align (http://miso.readthedocs.org/en/fastmiso/#alternative-event-annotations). Why I don't understand.     ...
written 6.4 years ago by Anil Kesarwani • 90
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How to run MISO with ENSEMBL GTF if reads were aligned against UCSC genome
... Hi, I aligned reads against UCSC genome using STAR, where UCSC gtf was used as reference annotation. However, I want to do quantitation of splicing event as per in ENSEML gtf file using MISO tool.  In the homepage of MISO, it has been suggested to re-align the reads with the genome build prepared w ...
tool rna-seq written 6.4 years ago by Anil Kesarwani • 90 • updated 3.7 years ago by lavanya.kannan • 10
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Comment: C: How does the insert size parameter change after trimming (MATS tool)
... I used Picard to calculate the average length of reads and standard deviation in each sample, which seem to be critical parameters for MATS ...
written 6.4 years ago by Anil Kesarwani • 90

Latest awards to Anil Kesarwani

Popular Question 4.5 years ago, created a question with more than 1,000 views. For How to count novel and known splice junction reads from BAM
Popular Question 4.5 years ago, created a question with more than 1,000 views. For How does the insert size parameter change after trimming (MATS tool)
Popular Question 4.5 years ago, created a question with more than 1,000 views. For How does MISO quantify genes with single isoform
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Extraction of splicing events and their quantification
Popular Question 4.5 years ago, created a question with more than 1,000 views. For rMATS: quantification of differential splicing
Popular Question 4.6 years ago, created a question with more than 1,000 views. For How does the insert size parameter change after trimming (MATS tool)
Popular Question 4.9 years ago, created a question with more than 1,000 views. For How does the insert size parameter change after trimming (MATS tool)
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