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Galaxy "Stitch Maf Blocks" Produced Null Bases

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.

galaxy maf

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