S288c Genome Chip

 

In-house Software

QA_grid3.pl

This program produces an assessment of gridding quality by extracting and listing the checkerboard 'B2' features from the tiling chip. The common use version of this program is on the LINUX computer , Sequence. To use QA_grid3.pl you need an SGTC unix account. Once logged in:

localhost:~/projects/yeast_chip curtis$ ./QA_Grid3.pl
Program uses .SGTC1lq & .CEL file as input
the *.SGTC1lq files has the locations of the grid features and is specific to the type of chip
you need different SGTC1lq files for the tiling or S98 chip
this program writes to STDOUT, so if you don't want output to screen, redirect to file:
/tools/bio/bin/QA_Grid3.pl </tools/bio/bin/*.SGTC1lq> <cel_file> > outputfile
for example, for a S98 cel file named mycel.CEL:
/tools/bio/bin/QA_Grid3.pl /tools/bio/bin/default_S98.SGTC1lq mycel.CEL > mycel.CEL.out
for a tilng chip cel file named myTile.CEL:
/tools/bio/bin/QA_Grid3.pl /tools/bio/bin/default_tiling.SGTC1lq myTIle.CEL > myTile.CEL.out
output of this file is 5 columns of tab-delimited text:
x y off_intensity on_intensity on-(prev_off_intensity)
each xy location corresponds to either an off or on probe, so only on off these columns has a value for any given line
in addition, the difference is only calculated if the previous off probe is adjacent to the current on probe

extractCommonInten.pl

This program extracts the intensities for all probes (yeast sequences, not controls) in common between the S98 chip and the yeast tiling chip. The common use version of this program is on the LINUX computer , Sequence. To use extractCommonInten.pl you need an SGTC unix account. Once logged in:

Program uses two .CEL files and a custom text file as input
the first CEL file is from an S98 chip and the second a yeast tiling chip
the third file contains the coordinates of the common probes, a current (11/29/04) version
of this file is called tile_S98Common.txt
this program writes to STDOUT, so if you don't want output to screen, redirect to file:
/tools/bio/bin/extractCommonInten.pl <S98Celfile> <tilingCEL file> </tools/bio/bin/tile_S98Common.txt> > outputfile
for example, for a S98 & tiling cel files named myexp
/tools/bio/bin/extractCommonInten.pl myexp_S98.CEL myexp_tiling.CEL /tools/bio/bin/tile_S98Common.txt > myexp_s98_tilie.out.txt
output of this program is tab-delimited text, the first row is a header row describing the columns:
seq chrNum chrPos strand tile_PMx tile_PMy tile_PMmean tile_PMstdd tile_PMpix tile_MMx tile_MMy tile_MMmean tile_MMstddtile_MMpix S98_id S98pos S98_PMx S98_PMy S98_PMmean S98_PMstdd S98_PMpix S98_MMx S98MMy S98MMmean S98MMstdd S98MMpix
a description of the fields:
field description
seq      probe seq
chrNum      chromosome #
chrPos      nuc position on chromosome, this is from 1lq file pos of MM base
strand      strand (forward or reverse of probe) relative to chromosome
tile_PMx      x coordinate of PM probe on tiling chip
tile_PMy      y coordinate of PM probe on tiling chip
tile_PMmean      intensity of PM (from cel file, mean of pixels)
tile_PMstdd      standard deviations of tile_PMmean (from cel file)
tile_PMpix      number of pixels used for tile_PMmean (from cel file)
tile_MMx      x coordinate of MM probe on tiling chip
tile_MMy      y coordinate of MM probe on tiling chip
tile_MMmean      intensity of MM (from cel file, mean of pixels)
tile_MMstdd      standard deviations of tile_MMmean (from cel file)
tile_MMpix     number of pixels used for tile_MMmean (from cel file)
S98_id      affy id for ORF on s98 chip, from 1lq file, there is an affy file that
          gives a more useful name(genbank# or some other id) for this
          but i havent had time to parse this data.
S98pos      pos of probe in S98_id seq.
S98_PMx      x coordinate of PM probe on S98 chip
S98_PMy      y coordinate of PM probe on S98 chip
S98_PMmean      intensity of PM (from cel file, mean of pixels)
S98_PMstdd      standard deviations of tile_PMmean (from cel file)
S98_PMpix      number of pixels used for tile_PMmean (from cel file)
S98_MMx      x coordinate of MM probe on S98 chip
S98_MMy      y coordinate of MM probe on S98 chip
S98_MMmean      intensity of MM (from cel file, mean of pixels)
S98_MMstdd      standard deviations of tile_MMmean (from cel file)
S98_MMpix      number of pixels used for tile_MMmean (from cel file)

extractControlInten.pll

There are two different control intensity files, controlLocs.txt and At_controlLocs.txt that contains only the Arabidopsis control probe on the chip. Here is a list of the control probes on the chip using the Affymetrix names:

AFFX-BioB-5 20 probe pair set sense
AFFX-BioB-M 20 probe pair set sense
AFFX-BioB-3 20 probe pair set sense
AFFX-BioC-5 20 probe pair set sense
AFFX-BioC-3 20 probe pair set sense
AFFX-BioDn-5 20 probe pair set sense
AFFX-BioDn-3 20 probe pair set sense
AFFX-CreX-5 20 probe pair set sense
AFFX-CreX-3 20 probe pair set sense
AFFX-BioB-5 20 probe pair set antisense
AFFX-BioB-M 20 probe pair set antisense
AFFX-BioB-3 20 probe pair set antisense
AFFX-BioC-5 20 probe pair set antisense
AFFX-BioC-3 20 probe pair set antisense
AFFX-BioDn-5 20 probe pair set antisense
AFFX-BioDn-3 20 probe pair set antisense
AFFX-CreX-5 20 probe pair set antisense
AFFX-CreX-3 20 probe pair set antisense
AFFX-r2-TagA_x 11 probe pair set sense
AFFX-r2-TagB_x 11 probe pair set sense
AFFX-r2-TagC_x 11 probe pair set sense
AFFX-r2-TagD_x 11 probe pair set sense
AFFX-r2-TagE_x 11 probe pair set sense
AFFX-r2-TagF_x 11 probe pair set sense
AFFX-r2-TagG_x 11 probe pair set sense
AFFX-r2-TagH_x 11 probe pair set sense
AFFX-r2-TagIN-3_x 11 probe pair set sense
AFFX-r2-TagIN-5_x 11 probe pair set sense
AFFX-r2-TagIN-M_x 11 probe pair set sense
AFFX-r2-TagJ-3_x 11 probe pair set sense
AFFX-r2-TagJ-5_x 11 probe pair set sense
AFFX-r2-TagO-3_x 11 probe pair set sense
AFFX-r2-TagO-5_x 11 probe pair set sense
AFFX-r2-TagQ-3_x 11 probe pair set sense
AFFX-r2-TagQ-5_x 11 probe pair set sense
AFFX-r2-TagA_x 11 probe pair set antisense
AFFX-r2-TagB_x 11 probe pair set antisense
AFFX-r2-TagC_x 11 probe pair set antisense
AFFX-r2-TagD_x 11 probe pair set antisense
AFFX-r2-TagE_x 11 probe pair set antisense
AFFX-r2-TagF_x 11 probe pair set antisense
AFFX-r2-TagG_x 11 probe pair set antisense
AFFX-r2-TagH_x 11 probe pair set antisense
AFFX-r2-TagIN-3_x 11 probe pair set antisense
AFFX-r2-TagIN-5_x 11 probe pair set antisense
AFFX-r2-TagIN-M_x 11 probe pair set antisense
AFFX-r2-TagJ-3_x 11 probe pair set antisense
AFFX-r2-TagJ-5_x 11 probe pair set antisense
AFFX-r2-TagO-3_x 11 probe pair set antisense
AFFX-r2-TagO-5_x 11 probe pair set antisense
AFFX-r2-TagQ-3_x 11 probe pair set antisense
AFFX-r2-TagQ-5_x 11 probe pair set antisense
AF159801 one probe every one base sense
AF159803 one probe every one base sense
AF168390 one probe every one base sense
AF191028 one probe every one base sense
AF198054 one probe every one base sense
AF247559 one probe every one base sense
deleted_thr_3 one probe every one base sense
deleted_thr_5 one probe every one base sense
deleted_trp one probe every one base sense
NM_002046 one probe every one base sense
present_thr one probe every one base sense
present_trp one probe every one base sense
X56062 one probe every one base sense
X58149 one probe every one base sense
AF159801 one probe every one base antisense
AF159803 one probe every one base antisense
AF168390 one probe every one base antisense
AF191028 one probe every one base antisense
AF198054 one probe every one base antisense
AF247559 one probe every one base antisense
deleted_thr_3 one probe every one base antisense
deleted_thr_5 one probe every one base antisense
deleted_trp one probe every one base antisense
NM_002046 one probe every one base antisense
present_thr one probe every one base antisense
present_trp one probe every one base antisense
X56062 one probe every one base antisense
X58149 one probe every one base antisense

 

This program extracts the intensities for control probes specified in an input file. The common use version of this program is on the LINUX computer , Sequence. To use extractControlInten.pl you need an SGTC unix account. Once logged in:

 

Program uses controlLocs.txt & .CEL file as input the controlLocs.txt file has the locations of the control features. this program writes to STDOUT, so if you don't want output to screen, redirect to file: /tools/bio/bin/extractControlInten.pl "cel_file" outputfile for a tiling chip cel file named myTile.CEL:

/tools/bio/bin/extractControlInten.pl /tools/bio/bin/controlLocs.txt myTIle.CEL > myTile.CEL_controls.out

 

/tools/bio/bin/extractControlInten.pl /tools/bio/bin/At_controlLocs.txt myTIle.CEL > myTile.CEL_controls.out

output of this file is 8 columns of tab-delimited text: affy_id probe_pos PMinten PM_stdd PM_pixels MM_inten MM_stdd MM_pixels the controlLocs.txt is made by a specialized script that parses the .SGTC1lq file so if you need a different set of controls, let me know I a can create a different input file