User: manojkumar_bhosale

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Posts by manojkumar_bhosale

<prev • 18 results • page 1 of 2 • next >
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What is the difference between VCF specifications 4.1 and 4.2?
... I want to convert VCF rom 4.1 to 4.2 format. What changes are needed to make this happen? Also, is there any tool which can do this conversion? Is there any tool to validate if 4.2 format file follows 4.2 specifications? Any help will be really appreciated. ...
vcf next-gen sequencing written 7 months ago by manojkumar_bhosale60 • updated 5 months ago by Biostar ♦♦ 20
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... Well, that line is just the declaration of variable named "pref" which is used in code below wherever the file name prefix is required. Simply put, its used to create file name prefix. For example, below line will assign variable "idxpref" with value "rn6.softmask.all_index" idxpref="${pref}_ind ...
written 7 months ago by manojkumar_bhosale60
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What is the algorithm used by UCSC lift over tool?
... I want to write my own tool for liftover between two genome assemblies. Please let me know how the chain file is used to convert the coordinates? ...
assembly alignment sequencing written 7 months ago by manojkumar_bhosale60
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Comment: A: Where can I get ?or how can I make a mappability track for hg38 assembly
... "rn6.softmask.all.fa" is the reference genome file with repetitive regions soft masked. ...
written 7 months ago by manojkumar_bhosale60
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Comment: C: I want to convert IGVs TDF file to a readable (.txt) format. Is there any tool/
... Thanks for the prompt reply !! I tried the above command but it looks like its giving me total number of bases(depth/coverage) at each locus. But I want count of each base covering each location e.g. chr7:1000 is covered by A:10, T:20, G:30,C:40 bases. Is there a way it can be done? ...
written 2.3 years ago by manojkumar_bhosale60
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I want to convert IGVs TDF file to a readable (.txt) format. Is there any tool/ library available for it?
... I searched the IGV website but they have tools to convert TDF to wig, bigwig formats and these are all binary files. I want to read the TDF file and find the count of the bases at each location in my target region. If its not possible then is there any other way to achieve it? ...
next-gen alignment bam igv written 2.3 years ago by manojkumar_bhosale60 • updated 2.3 years ago by dariober9.2k
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... Thank you very much !! You saved me lot of efforts. ...
written 2.3 years ago by manojkumar_bhosale60
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... My mistake !! I looked it in binary-pre-release-2, which does not have the binary for mappability but release 3 has it. Thanks !! ...
written 2.3 years ago by manojkumar_bhosale60
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Where can I get ?or how can I make a mappability track for hg38 assembly
... How can I make a mappability track for hg38 assembly. I have explored the GEM library option to generate the mappability track but the software does not have binary for generating mappability track(http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030377). It will be very helpful if ...
assembly sequence alignment sequencing written 2.4 years ago by manojkumar_bhosale60 • updated 4 days ago by shashankbic10
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Comment: C: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... With the release of hg38 need to revisit contents of this post!! :) ...
written 2.4 years ago by manojkumar_bhosale60

Latest awards to manojkumar_bhosale

Popular Question 18 months ago, created a question with more than 1,000 views. For Where can I get ?or how can I make a mappability track for hg38 assembly
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Error while running Varscan copynumber command
Scholar 3.1 years ago, created an answer that has been accepted. For A: List of nuclear genes involved in mitochondrial processes
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: About gene id

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