Hello,

The regions in your BED file appear to be representing non-coding transcripts, which is why there is no output using this specific tool. A better choice would be the tool " Stitch MAF blocks".

Hopefully this helps. Next time, please only post to a single list. For usage questions like this one, the galaxy-user@bx.psu.edu mailing list is best.
http://wiki.galaxyproject.org/Support#Mailing_Lists

Thanks!

Jen
Galaxy team

On 11/29/12 4:03 AM, 张坤山 wrote:

Hi all,

I trying to stitch some MAF from bed12 file using "Stitch Gene blocks".

Galaxy successfully recognized my BED file and finished stitch, but no sequence in the result.

My BED file is like:

chr1 14662810 14707010 TCONS_00007949 0 - 14707010 14707010 0 5 229,139,106,162,77, 0,4387,4975,8271,44123,

chr1 84928679 84942052 TCONS_00027714 0 + 84942052 84942052 0 4 64,173,111,398, 0,1330,12292,12975,

chr1 91200237 91254779 TCONS_00030473 0 - 91254779 91254779 0 3 285,177,104, 0,52636,54438,

I choose 36 mammals to stitch blocks.

Galaxy gives me result like:

>mm9.TCONS_00007949

>hg19.TCONS_00007949

>panTro2.TCONS_00007949

No sequence in result.What happen??

Kunshan
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