User: Jitendra

gravatar for Jitendra
Jitendra50
Reputation:
50
Status:
New User
Location:
India
Website:
http://www.bioinformat...
Last seen:
6 years, 1 month ago
Joined:
8 years, 1 month ago
Email:
j*********@gmail.com

Posts by Jitendra

<prev • 4 results • page 1 of 1 • next >
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Extracting Individual Allele Frequencies From A Vcf File
... Hi all, I have used SAMtools to identify SNPs within 3 separate individuals and have generated a VCF file. I am able to extract the depth for each individual but am struggling to get the allele frequency at each SNP for each individual. The VCF contains an overall alternative allele frequency but I ...
vcf samtools snp written 6.9 years ago by Jitendra50 • updated 6.9 years ago by Maxime Lamontagne2.1k
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Answer: A: Generating .Vcf.Idx Files From Cmdline
... Hi I found IGVTools, best for VCF indexing. igvtools can be run from the command line or IGV itself (File>Run igvtools...) After launching, choose the Index command and browse to your .vcf file. The index file (.idx) will be created in the same directory as the .vcf file. Thanks! Jitendra ...
written 6.9 years ago by Jitendra50
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Scary Exon Sizes
... Hi BioStars, Followings are the part of Cufflinks output (transcripts.gtf). The last column, added by me, is the length of the transcripts and exons. Can we get an exon of size 7 and transcripts of 124700 size? Chr1 Cufflinks transcript 210626 210717 1000 91 Chr1 Cufflinks ...
gtf cufflinks written 7.1 years ago by Jitendra50 • updated 7.1 years ago by Gww2.6k
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Answer: A: Tophat Stalled Error = -9
... Hi! this could be not-enough-memory error. Maybe you can try mapping the data set in smaller chunks and then merge the bam files at the end? ...
written 7.2 years ago by Jitendra50

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