Hi! Having provided a name (field 4) in a UCSC bed file ( http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1 ) and sought a RefSeq name using the UCSC Table Browser ( http://www.genome.ucsc.edu/cgi-bin/hgTables ), I would now like to recover which line of the bed file delivered which line of the output file… However, I am told I need Galaxy to provide a workflow to do this. Can anyone explain how? eg, one line of my bedfile looks like: chr2 2723752 2723777 seqid6354405 0 - and one line of my intersected table browser output looks like: chr1 176432306 176811970 NM_020318 0 + 176525458 176811590 0 23 248,1835,1072,146,294,193,122,490,129,92,194,147,136,217,172,178,214,169,136,110,72,99,455, 0,92236,131353,207799,226966,228955,232567,235929,239436,243188,246812,248664,276455,276809,302495,306436,307796,326638,328176,330389,336890,377002,379209,
Clearly the first line of my bed doesn't correspond to the first line of my intersection output, but as my bed is long, what reference can I use to unambiguously identify which line of output the first line of my intersection corresponds to? How do I do this in Galaxy? PS - I tried this workflow earlier today without success, aiming to achieve a similar objective: https://usegalaxy.org/u/james/w/workflow-from-ucsc-genes-and-symbols PPS- I also note similar issues were raised in this discussion, with Galaxy promoted as the solution, but with no real details about how to achieve the desired results: http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10615&S=0d1b303e6dfdceaf3b240804fd0f52aa Bert Gold, Ph.D., FACMG Staff Scientist NCI-Frederick Frederick, MD 21702 VOICE: 301-846-5098 EMAIL: go...@mail.nih.gov ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
