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2013-09-15 16:45:39 -0600 asked a question what does "intronic depth" mean in tophat alignment visual?


I have generated tophat alignment from RNAseq data with default settings. When I visualize the alignment on Golden Helix genome browse, I notice these light grey stacked pile of reads labeled as "intronic depth". These seem to typically map over intronic regions and have a good coverage but I can't see the base or any other information related to it. For instance, I have a position in the mapped alignment happen to be in a coding gene exonic region marked with:

match G 2 reads mismatch A 20 reads intronic 150 reads

Does anyone know what does this "intronic depth" means? How can I explain these intronic reads in a coding region where I see a somatic change? are these of concern? should such site with a variant be considered as genuine?

I would appreciate any feedback or help. Thank you!


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2013-05-16 15:45:34 -0600 asked a question Feature to filter out known SNPs (SNPs with rs#) from the vcf file using SNP analysis package?

Given a vcf file, is there a feature in SNP analysis package to filter out known SNPs (SNPs with rs# associated with)? If so, how is it done? Is it simply the concordance between the variant call in the vcf file to the known SNP in the dbSNP 137 build by chromosome#, position, reference, and alternate allele?

I want to filter out any known and common SNPs present in dbSNP or Thousand Genomes from my vcf file to get to the nvel SNPs. I am noticing discrepancies in the tools out there that provide any dbSNP validation versus the SNPs listed in the dbSNP 137 build file itself (downloaded from ncbi ftp). For example, for a given variant, if I do not find a SNP in the dbSNP 137 file, I end up finding an rs# associated with the same variant from a tool such as Polyphen-2 or SeattleSeq while I am searching for protein prediction. SNP analysis package by golden helix integrates these small multiple steps all in on one environment and I like that, however I want to know if I use SNP analysis package and don't find an rs# associated with my variant call, is it really so?.

Any feedback or comment will be appreciated!

Thank you!

Regards, BD

2013-05-16 15:24:37 -0600 asked a question How to visualize tandem duplications and translocations in GenomeBrowse?

I am interested in visualizing Internal Tandem Duplications in gene of interest from the aligned paired-end RNA-seq data. I am also interested in locating translocations including fusion genes. Is there a way to visualize these in GenomeBrowse by Golden Helix?