problem: "stitch MAF blocks" produced NULL bases
steps: From http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chrY:23310464,23331995
we got the following bases:
agtttacccaactcacaggtatttgaggatacaaacccatgactgggcttggctttaaaaattcctatctgaaatttctagt..........
We want to do multiple-species alignment using galaxy "stitch MAF blocks" . our BED file (human.bed) is:
> chrY 23310464 23331995 TCONS_00017641 0.0 + 23310464 23331995 0,0,0 4 17,54,135,154, 0,3010,4260,21377,
We use Galaxy "stitch MAF blocks" function on https://main.g2.bx.psu.edu/ . Get Data -> Upload File -> File Format: "bed", File: click and choose "human.bed", Genome: "Human Feb. 2009 (GRCh37/hg19) (hg19)" Fetch Alignments -> Stitch MAF blocks -> Choose intervals: "human.bed", MAF source: 46way.
we got:
>hg19.chrY(+):23310464-23331995
------------------------------------------------------------------------------------------...
>mm9
------------------------------------------------------------------------------------------...
>rn4
------------------------------------------------------------------------------------------..
We think the second line(below >hg19.chrY(+):23310464-23331995) should be "agtttacccaactcacaggtatttgaggatacaaacccatgactgggcttggc...", not "----------------...". What's wrong with our steps, or, are the results correct ? Thanks.
