Ok, thanks for the clarifications Jennifer.
Ignasi On Tue, Jun 22, 2010 at 8:00 PM, Jennifer Jackson <[email protected]> wrote: > Update with some clarification that applies to this track: > > The underlying RefSeq, NR_002930, has been updated since > the hg18 build, and is now version 2 rather than version 1. > The version 2 does not align with the one base gap. > > For non-refSeq sequence we would merge out this gap, but > we take refSeq literally, and this escapes the merging. > > Regards, > Jen > > > On 6/18/10 6:40 PM, Jennifer Jackson wrote: > >> Hello, >> >> What you are detecting in the alignments is the presence of bases in the >> aligned mRNA sequence that are not in the reference genome. BLAT will >> break the alignment into two blocks at these insertion locations. This >> is both an expected and a normal part of the track contents. >> >> I hope this information is helpful. Please feel free to contact the >> help mailing list again if you require further assistance. >> >> Best regards, >> Jen >> >> UCSC Genome Browser Support >> http://genome.ucsc.edu/contacts.html >> [email protected] [email protected] >> >> On 6/18/10 9:11 AM, Ignasi Moran Gmail wrote: >> >>> Hey all, >>> >>> I found this bug in at least 58 of the genes of the kown_genes table for >>> hg18, where a single exon is reported as 2 separated exons, with a 0 >>> bases >>> long intron in between. For example, >>> >>> uc001gxp.2 chr1 + 200403801 200425104 200403801 >>> 200403801 23 >>> >>> 200403801,200404372,200405064,200405531,200406935,200407291,200412799,200413270,200415861,200417408,200417639,200418878,200419134,200419317,200420432,200422011,200422283,200422753,200422758,200423019,200423213,200424577,200424981, >>> >>> 200404262,200404421,200405333,200405795,200407190,200407537,200413084,200413689,200416140,200417535,200417687,200418972,200419225,200419410,200420530,200422180,200422442,200422758,200422890,200423107,200423292,200424743,200425104, >>> >>> This gene has 23 reported exons, however, there is one starting at >>> >>> chr1:200422753-200422758 >>> >>> and the next one is reported at >>> >>> chr1:200422758-200422890 >>> >>> Attached I send you the list with all the ucsc gene names where I could >>> find >>> this behaviur happening at least once. I'm not confident the list is >>> complete though. >>> >>> Hope I'm reporting this on the right place. >>> >>> >>> Cheers, >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > -- Ignasi Moran Castany PhD Student - Jorge Ferrer's lab IDIBAPS - Hospital Clínic de Barcelona http://betacellregulation.net _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
