User: Gireesh K. Bogu

gravatar for Gireesh K. Bogu
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Singapore
Last seen:
7 years, 2 months ago
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7 years, 3 months ago
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Bioinformatics Specialist, Genome Institute of Singapore

Posts by Gireesh K. Bogu

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Cufflinks Transcript Assembly
... how about single exon transcripts ? ...
written 7.2 years ago by Gireesh K. Bogu100
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Comment: C: Why Does Ucsc Refseq Gene Annotation File Have More Than One Annotation For A Sa
... why don't u post an example? ...
written 7.2 years ago by Gireesh K. Bogu100
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Comment: C: Why Does Ucsc Refseq Gene Annotation File Have More Than One Annotation For A Sa
... can you give any example ? ...
written 7.2 years ago by Gireesh K. Bogu100
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Answer: A: Database To Find Intron Sequences ?
... Well you didn't specify which species you need to extract introns. Anyway there is a simple trick in Galaxy where you can use "Extract Features" to convert gene to exon/intron/codon regions. This works only if you have a known gene list in BED format. Alternatively you can look into kent tools. Good ...
written 7.2 years ago by Gireesh K. Bogu100
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Answer: A: Predictability Of Regulatory States In New Cell Lines Or Tissues From Existing E
... May be not, as chromatin states are specific to regulatory elements that are tissue/cell specific. Also I would like to add, there are so many regions in the human genome that are not covered by any of these 15 chromatin states predicted by using 8 histone and 1 ctcf marks may lower your predictive ...
written 7.2 years ago by Gireesh K. Bogu100
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Answer: A: Rpkm Calculation
... As @RM mentioned before you can flag stats to count the number of mapped reads. There are many tools to calculate RPKM. You can use ERANGE for example. However FPKM is an improved version of RPKM that remove biases more efficiently. For this you can use Cufflinks. ...
written 7.2 years ago by Gireesh K. Bogu100
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Comment: C: 1000 Genomes Ld Calculation
... I tried 1st tabix command using a bed file of GWAS snps but I got the following error "ti_index_core] the indexes overlap or are out of bounds". I used hg19_gwas_snps.bed and hg19 1kg data ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ ...
written 7.2 years ago by Gireesh K. Bogu100
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Comment: C: 1000 Genomes Ld Calculation
... I tried this using a bed file of GWAS snps but I got the following error "ti_index_core] the indexes overlap or are out of bounds". I used hg19_gwas_snps.bed and hg19 1kg data ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ ...
written 7.2 years ago by Gireesh K. Bogu100
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Comment: C: What Is The Best And Fastest Way Of Uploading Wiggle Files Into Ucsc Browser ?
... Yes. Thanx. I totally missed this article about bigWig ("BigWig and BigBed: enabling browsing of large distributed datasets") ...
written 7.2 years ago by Gireesh K. Bogu100
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Comment: C: What Is The Best And Fastest Way Of Uploading Wiggle Files Into Ucsc Browser ?
... Yes. Thanx. I totally missed this article about bigWig ("BigWig and BigBed: enabling browsing of large distributed datasets"). However, I am unable to upload my bedGraph files or bigWig files into UCSC. I created these by using the following 2 commands using Kent tools. (1) sort -k1,1 -k2,2n R15.bed ...
written 7.2 years ago by Gireesh K. Bogu100

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