S288c Genome Chip

 

bpmap files

 

bpmap files are a binary format file that is used for input with Affymetrix's GTRANS, renamed Tiling Analysis Software, genome tiling chip analysis program. The files contain information about a probe's x,y location on the chip and its location on a chromosome. This input file, along with cel files, is used by GTRANS to analyze genome tiling chips. The figure at the top of the tiling chip main page shows GTRANS output displayed in IGB.

Affymetrix sent us bpmap files that contained all of the S288c probes, forward and reverse in one file, and included the location of each instance of probe sequence in the genome, including locations that were not part of the 8bp (per strand) tile. The time needed for calculations increases in a nonlinear fashion as number of probes with the same sequence mapped to different locations in the genome increases. Using the default settings on GTRANS, GTRANS runs in 10's of hours to run. This time can be decreased by reducing the window size in GTRANS options. The initial file from Affymetrix contained all probes, including the mapping of all repetitive probes to all locations ("bonus probes", the probe sequence contained in the genome but not in the frame that the genome is tiled on the chip) in the genome. Excluding the mapping of the repetitive probes (around 109,000 probe pairs out of 3,018,000 probe pairs) to all locations in the genome from the bpmap files allows the analysis to run much faster, a minute or two for one strand of the entire genome. In addition, the forward and reverse probes are put in separate files, so that strand specific hybridization can be investigated. The Affymetrix convention of designating stand specificity by target is used. The file names ( 2005Jan_S288c_Uni_R.bpmap) specify the version (Version 1 or2005Jan) of the sequence to which the probes are mapped and whether the file contains all probes (All) or only the unique (Uni) probes and if the file contains the probes that hybridize to forward target (F) 0r reverse target (R). It is left to the user to decide if they feel useful information can be obtained form the repetitive probes. A gff file (for use in IGB) that details the locations of the probes that are present more than once in the genome is also provided.

The bpmap files are also provided in versions that map to the different versions of the S288c genome. You should use a bpmap file that corresponds to the version of sequence for your other data files, fasta, gff, etc.

All files contain data for the S288c genome (16 chromosomes + mitochondria), YJM189 unique sequences and the Arabidopsis control cDNA sequences.

With the release of the 7G scanner, Affymetrix has supplied a bpmap file compatible with 7G output. It contains all sequences on the chip, including controls (271 different sequences, the S288c forward and reverse strands are analyzed separately with this file).

Files with "rotated" in their name are compatable with data generated by the updated 7G scanner.

 

 

File name
(downloadable, zipped, 2 files, one each for forward & reverse probes, exept affy and BothStrands bpmap files are one file each)
Description
2006Feb All 7G All probes, genome coordinates relative to Feb. 2006 version of sequence. Rotated for use with 7G scanner
Version 1 All All probes, genome coordinates relative to Version 1 of sequence.
2005Jan All All probes, genome coordinates relative to Jan. 2005 version of sequence.
2006Feb All Both Strands 7G All probes, both stands together, for double stranded labeling, genome coordinates relative to Feb. 2006 version of sequence. Compatible with data from the updated 7G scanner
2006Feb Unique Both Strands 7G Unique probes, both stands together, for double stranded labeling, genome coordinates relative to Feb. 2006 version of sequence. Compatible with data from the updated 7G scanner
2006Feb All Both Strands All probes, both stands together, for double stranded labeling, genome coordinates relative to Feb. 2006 version of sequence.
2005Jan Unique Unique probes, genome coordinates relative to Jan. 2005 version of sequence.
Affymetrix bpmap rotated Affymetrix's bpmap file, all sequences on chip relative to Version 1 of sequence. Compatible with data from the updated 7G scanner
Version 1 Unique Unique probes, genome coordinates relative to Version 1 of sequence.
2005Jan Unique Unique probes, genome coordinates relative to Jan. 2005 version of sequence.
Affymetrix bpmap Affymetrix's bpmap file, all sequences on chip relative to Version 1 of sequence.
Affymetrix bpmap all probes mapped Affymetrix's bpmap file, all sequences on chip relative to Version 1 of sequence. probes that have multiple locations in genome are mapped to all locations in this file.

 

These files use the affy convention for labeling forward and reverse. F or R refers to the target strand and not the sequence is on the chip.