Hi Jen, Thanks a lot for your reply! So please see the following bed file. track name=junctions description="TopHat junctions" chr19 3262083 3264847 JUNC00000001 2 - 3262083 3264847 255,0,0 2 61,37 0,2727 chr19 3266410 3267296 JUNC00000002 2 - 3266410 3267296 255,0,0 2 49,55 0,831 chr19 3267271 3268345 JUNC00000003 3 - 3267271 3268345 255,0,0 2 65,48 0,1026 chr19 3268383 3268720 JUNC00000004 2 - 3268383 3268720 255,0,0 2 33,61 0,276 chr19 3272970 3274417 JUNC00000005 5 - 3272970 3274417 255,0,0 2 65,62 0,1385 chr19 3274528 3276802 JUNC00000006 1 - 3274528 3276802 255,0,0 2 28,47 0,2227 chr19 3276860 3279592 JUNC00000007 4 - 3276860 3279592 255,0,0 2 59,60 0,2672 chr19 3279962 3281488 JUNC00000008 2 - 3279962 3281488 255,0,0 2 34,70 0,1456 chr19 3281520 3282759 JUNC00000009 2 - 3281520 3282759 255,0,0 2 68,59 0,1180 chr19 3284771 3285362 JUNC00000010 2 + 3284771 3285362 255,0,0 2 46,53 0,538 chr19 3284779 3285344 JUNC00000011 2 + 3284779 3285344 255,0,0 2 54,35 0,530 chr19 3285352 3286924 JUNC00000012 2 + 3285352 3286924 255,0,0 2 43,50 0,1522 chr19 3289043 3291029 JUNC00000013 5 + 3289043 3291029 255,0,0 2 44,53 0,1933 I have stimulated sample and control sample, I would like to know if there is 3 UTR, 5 start site variance in the stimulated sample. There is always some interesting info in the 3 UTR. If the length of 3UTR changes under specific biological condition, then it could explain some mechanism, for example some microRNA info. And so far, I uploaded the bed file to Galaxy, and choose from cdsEnd to txEnd (should be transcript end, right?) which should be 3 UTR info. If this is right, I check by hand every 3UTR of every gene compared with public annotation like UCSC. But this is not a proper way and time-consuming. I do not have bioinfomatics experience, do not know if one can give me some advice how to do this properly. Many thanks for your help! Best, Wei On 6/22/10 6:35 PM, Jennifer Jackson wrote:
Hi Wei,
Could you explain in more detail the type of analysis that you are interested in doing? Including a few lines of the BED file (5-10) pasted into the reply would be helpful.
Thanks,
Jen Galaxy Tea
On 6/10/10 11:14 AM, Yanwei Tan wrote:
Deal all,
I was wondering if anyone know Galaxy can analyze the New 5' start site, 3' end site and long internal coding exons. Because I just try to run Scripture (http://www.broadinstitute.org/software/scripture/Graph%20building) and got the bed file. Can someone give me some hint?
Many thanks in advance! Wei _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user