Hi,

I am bothered by an error/bug during the usage of Galaxy (it's daily-used tool for me. Thanks) --- it seems that the strand information is not taken into consideration when getting the "Overlapping pieces of Intervals" by doing the intersection of two queries. To focus on the problem, I  make a minimal dataset here:  first and second in the following BED track file.  I also listed the intersected results from Galaxy. You can test it by past the each dataset into Galaxy and do intersection ("Overlapping pieces of Intervals" of first query that intersect second query)


You can see the problem easily if you view the following track in USCS browser (hg18): the two forward (+) regions in first query should be only intersected with the forward (+) regions in second query, NOT regions on reverse strand. That's my understanding to intersection. Isn't right? From the result, it seems that each region in first query is intersected with each region in second query (NO MATTER its strand). I think if my understanding is correct, this should be correct soon, since intersection is such a widely used tool in Galaxy.

Thanks

browser position chr9:35799363-35799773
track name="first" description="first query" visibility=2 color=255,0,0
chr9  35799401  35799509  ENSE00001149735  0  -
chr9  35799377  35799729  ENSE00001383867  0  +
chr9  35799377  35799729  ENSE00001476040  0  +

track name="second" description="second query" visibility=2 color=0,255,0
chr9  35799376  35799442  CCDS6590.1_cds_21_0_chr9_35799377_f  0  +
chr9  35799400  35799509  CCDS6592.1_cds_1_0_chr9_35799401_r  0  -

track name="intersect" description="Overlapping pieces of Intervals (from Galaxy)" visibility=2 color=0,0,255
chr9  35799401  35799509  ENSE00001149735  7  -
chr9  35799377  35799509  ENSE00001383867  22  +
chr9  35799377  35799509  ENSE00001476040  21  +


Xianjun
-- 
==========================================
Xianjun Dong
PhD student, Lenhard group
Computational Biology Unit
Bergen Center for Computational Science
University of Bergen
Hoyteknologisenteret, Thormohlensgate 55
N-5008 Bergen, Norway
E-mail: xianjun.dong@bccs.uib.no
Tel.: +47 555 84022
Fax : +47 555 84295
==========================================