Hello Bremen, We cannot offer advice about roast.
But regarding sorting, in our process it is taken care of at the chaining step. The net step makes a single-coverage set of alignments which I believe is also important for multiz -- and definitely for phastCons. Since you are not chaining and netting, our processing is different to achieve input for multiz/phastCons. Examining the makedoc for hg19 could help. It has all of the exact commands we used to generate the Conservation track. This is in the kent source tree at: kent/src/hg/makeDb/doc/hg19.txt http://genome.ucsc.edu/FAQ/FAQdownloads.html#download27 A good place to ask for tool help might be the team that hosts Galaxy (PSU) to see if there is another way to ensure a single-coverage MAF (if you are not already filtering for single-coverage after sorting). http://g2.bx.psu.edu/ [email protected] Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/22/10 10:14 AM, Bremen Braun wrote: > Hi all, > I'm having trouble getting my alignments recognized with PhastCons. I > generated n alignments using lastz, did some filtering steps, and then used > multiz n-1 times to get a file which are queries aligned to the same target. > I generated a phylogenic tree with PhyloFit and this worked, but when I fed > this all to phastCons, I'd get the following error: > warning: maf_read: MAF file must be sorted with respect to reference > sequence if store_order=TRUE. Ignoring out-of-order blocks > maf.c:323: failed assertion `idx_offset>= 0' > Abort trap > > I used maf_order on the file taken as input to phastCons but I still got > this error. I read somewhere that autoMZ can be used to generate a multiple > alignment that respects phylogenic tree info but I am unable to see sample > usage and the parameters are very vague. It looks like roast takes the same > kind of parameters in the same order as autoMZ and I know that tool has been > used for your data. Could you give me an example of how it's used? > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
