Not sure if this needs using Bioconductor. To get the chromosome position(in bp, Build36) for a BAC clone, eg 'RP11-189K9', I was following this post: http://article.gmane.org/gmane.science.biology.informatics.conductor/1 1360/match=bac+position But I only got this table: 'ftp://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/objects/BUILD.36. 1/initial_release/clone.q.gz' (Here is the first several lines of the table: #tax_idclone_id xref_idclone_name insert_accession insert_gi strain 9606 CloneID:1 RP11-1006M13 9606 CloneID:10 CTA-102N2 9606 CloneID:100 CTA-124G2 ) from which I can identify the CloneID '230700' for 'RP11-189K9', without any positional information; Where to go to get the additional dataset for positions, please? Thanks a lot in advance for your reply. AT

On Mon, Nov 17, 2008 at 1:53 PM, Al Tango <time.is.flying@gmail.com> wrote: > Not sure if this needs using Bioconductor. > > To get the chromosome position(in bp, Build36) for a BAC clone, eg > 'RP11-189K9', I was following this post: > > http://article.gmane.org/gmane.science.biology.informatics.conductor /11360/match=bac+position > > But I only got this table: > ' > ftp://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/objects/BUILD.36 .1/initial_release/clone.q.gz > ' > > (Here is the first several lines of the table: > #tax_idclone_id xref_idclone_name insert_accession insert_gi strain > > 9606 CloneID:1 RP11-1006M13 > 9606 CloneID:10 CTA-102N2 > 9606 CloneID:100 CTA-124G2 > ) > > from which I can identify the CloneID '230700' for 'RP11-189K9', > without any positional information; > Where to go to get the additional dataset for positions, please? > Why not use the BacEndPairs table at UCSC? http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/bacEndPairs.tx t.gz Lists BAC name and location. Sean [[alternative HTML version deleted]]