hg19 RNA info

Question

[serenabivona]

Hello!

I need information about the Transcriptome file for hg19, hg38 or similar files that can help me in my purpose. In brief, I have the coordinates of exons from a cds of my interest (starts and end positions) on hg19 and hg38.... ex: Chr. 9 start 130883969 end 130885683 ....but for my application I need to know these coordinates into the transcriptome to generates a file containing my target region to launch a run ngs. Can anyone help me, please??

please please please

Thank you!!

Answer 1

[tarek.mohamed]

Hi ,

You can use "BiomaRt" package to grab all information you need about about your exons. and you can use "BSgenome" package to extract the sequences of your target regions. "TxDb.Hsapiens.UCSC.hg19.knownGene" packge should be very helpful as well.

Tarek

[serenabivona]

Thank you for your answer. However, if it is possible, I would need more info...for example, using Biomart I found again only the position of my exon on chromosome, but not the corresponding position on the entire trapscriptome, if they exist. Maybe I don't know where exactly search and what kind of input give to the tools.

In summary, I need these positions to plun a run on PGM to analyze amplicons from cDNA, where amplicon overlaps more then one exon...

Thank you