Hi Vince, There is not a way to make BLAT join the two alignments. Rows in the axt alignment format (http://genome.ucsc.edu/goldenPath/help/axt.html) cannot contain gaps.
I hope this is helpful. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 3/30/12 7:09 AM, Vince Forgetta wrote: > > > Hi, > > I am using BLAT to align 454 reads back to an assembly that uses the > same reads. I noticed that the axt output breaks across two alignments, > while the psl output is within one line (see below). Is there a way to > report the axt output as one alignment? > > Thanks in advance for the help. > > Vince > > ** PSL OUTPUT ** > 381 2 0 0 5 9 9 13 + > GAC44FG01BFDF9 392 0 392 chrI 31789037 24269501 > 24269897 14 164,6,48,3,6,6,6,6,19,7,80,7,18,7, > 0,164,170,218,221,227,233,239,245,265,277,358,366,385, > 24269501,24269666,24269673,24269722,24269727,24269735,24269742,24269749,24269756,24269775,24269785,24269865,24269872,24269890, > > ** AXT OUTPUT ** > 0 chrI 24269502 24269782 GAC44FG01BFDF9 1 272 + 20942 > <ALIGNMENT> > > 1 chrI 24269786 24269897 GAC44FG01BFDF9 278 392 + 9145 > <ALIGNMENT> > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
