Charu: Please, direct these types of requests to mailing lists rather than to specific developers. The problem with adding the space of **** if that it will completely break the format definition, so this is not a good idea. If you want to enumerate clusters I would propose the following workflow: 1. Identify clusters (dataset 1) 2. Merge them using the "Operate on Genomic Intervals -> Merge" (dataset 2) 3. Add identifiers using the "Text manipulation -> Add column tool"(dataset 3) 4. Join your cluster (dataset 1) with dataset 3 using "operate on Genomic Intervals -> Join" This should solve your issue. Let me know if you have trouble. Thanks, anton galaxy team On Jul 21, 2009, at 6:41 PM, Charu Gupta Kumar wrote:

Dear Dr. Nekrutenko,

I was wondering if it would be possible to make a small change to the "Find cluster intervals, output grouped by clusters" tool (Find cluster intervals; output grouped by clusters is part of "Operate on Genomic Intervals"):

Ques.) Would it be possible to add a newline (or ***) after every cluster grouping, so users know when one cluster starts and another ends? It would be most helpful in figuring out the cluster demarcations.

Thanks so much,

Best regards,

Charu Charu Gupta Kumar, Ph.D.

******************

For example,

chr6_random 3253 3745 AA577868 0 + 3 chr6_random 3663 3896 BI789243 0 + 1 chr6_random 3663 4054 BM351966 0 + 1 chr6_random 3663 7171 CK903338 0 + 3 chr6_random 3847 7979 CK903339 0 - 4 chr6_random 3878 7963 BI962749 0 - 4 chr6_random 4062 7581 BM352279 0 - 4 chr6_random 4610 5058 AA828152 0 + 2 chr6_random 5243 5460 BM353279 0 - 2 chr6_random 5255 5403 BM314916 0 + 1 (space or ****** here) chr6_random 23107 23724 BU657553 0 - 1 chr6_random 23489 27653 BF507618 0 - 2 chr6_random 27113 27791 BI086568 0 + 9 chr6_random 70525 75802 BC064362 0 + 2 chr6_random 70514 73863 DA960595 0 + 3 chr6_random 70525 71258 BM470002 0 + 12

Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org