On Sun, May 10, 2009 at 7:13 AM, Wu, Xiwei <[email protected]> wrote: > Hi, > > I have aligned some Solexa RNA-seq data to refseq mRNA sequences. The > aligned location in the alignment report is relative to each refseq sequence > start. Is it possible to map the aligned results back to genome with current > available tools in Bioocnductor? In other words, I want to convert the > alignment position relative to genome location. It is relatively easy for > the exon sequences, but it is more complicated for the ones aligned to the > splicing junction. I think this is doable in R, but I just want to check to > see if there is already such a function avavilable. Thanks in advance. >
There isn't any high-level functionality like this in Bioconductor, as far as I know. It could probably be done fairly efficiently using the overlap functionality in IRanges. One trick would be to create a new coordinate system so that you can map all of the reads to exons in a single call to overlap(). In other words, virtually concatenate all of the transcripts, adding the appropriate offset to each read. Calling ranges() on the overlap() result gives you the intersecting part of the overlap. Then transform those coordinates to the genome. Essentially, you'll end up with a set of genomic ranges and an integer vector with the original read index for each range. Obviously, there were be duplicate indices whenever a read hit a splice junction. > Xiwei > > > > --------------------------------------------------------------------- > > SECURITY/CONFIDENTIALITY WARNING: > This message and any attachments are intended solely for the individual or > entity to which they are addressed. This communication may contain > information that is privileged, confidential, or exempt from disclosure > under applicable law (e.g., personal health information, research data, > financial information). Because this e-mail has been sent without > encryption, individuals other than the intended recipient may be able to > view the information, forward it to others or tamper with the information > without the knowledge or consent of the sender. If you are not the intended > recipient, or the employee or person responsible for delivering the message > to the intended recipient, any dissemination, distribution or copying of the > communication is strictly prohibited. If you received the communication in > error, please notify the sender immediately by replying to this message and > deleting the message and any accompanying files from your system. If, due to > the security risks, you do not wish to receive further communications via > e-mail, please reply to this message and inform the sender that you do not > wish to receive further e-mail from the sender. > --------------------------------------------------------------------- > > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
