Hi Adnan, This only occurs with translated blat and yes, you are correct. The strand in PSL format can be "-+" or "--" if the query (e.g. mRNA, EST) was sequenced in the antisense direction. It would then be aligning to either the positive strand (-+) or negative strand (--) of the target, which in this case is the genome.
Please feel free to contact the mail list again if you require further assistance. Best, Mary --------------------- Mary Goldman UCSC Bioinformatics Group On 9/2/10 8:20 AM, Derti, Adnan wrote: > Hi. > > Could you describe a scenario where the strand in PSL format would be > "-+" or "--"? Whether in files from UCSC or my own alignments, I only > ever see "++" or "+-". Would "-+" or "--" occur, say, for an EST > sequenced in antisense orientation? > > Thanks. > > Adnan > Notice: This e-mail message, together with any attachments, contains > information of Merck& Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
