After a successful run of RATools subdirectory should look like this:
RATools/ RATools/EXPERIMENT/ # User created experiment dir RATools/EXPERIMENT/BaseCaller/ # RATools created call dir
The experiment directory additionally contains the following files created during the run:
RATools/EXPERIMENT/EXPERIMENT.ref.fasta # see below RATools/EXPERIMENT/EXPERIMENT.txt # see below RATools/EXPERIMENT/alignment.txt # results of grid alignment RATools/EXPERIMENT/BaseCaller/*.fasta # fasta files for each image
Filename: Experiment.ref.fa
Location: EXPERIMENT Subdirectory
Contents: this file contains a fasta file of the reference sequence used to design the chip. It is created from the chip design file.
Filename: Experiment.txt
Location: EXPERIMENT Subdirectory
Contents: This file contains tab delimited data for the mean and variance of each probe for each dat file.
HEADER Line 1: CDF Filename EXPERIMENT.cdf Line 2: Dat Filenames EXPERIMENT_R1.DAT EXPERIMENT_R1_R2.DAT Line 3: Number of cols 5398 rows 5398 Line 4: Qualifier Expo Seq cbase pbase mean 242.794 npix mean BODY Column 1: Sequence Name Column 2: Position Column 4: Reference Sequence Column 5: Probe Sequence Row 1-3: Probes 1 - 3, non-reference bases on the reverse strand. Row 4: Probe 4 reference base on the reverse strand Row 5: Probe 5 reference base on the forward strand Row 6-8: Probes 6-8 non-reference bases on the forward stran DPGP_VECTAGS_1-0002 12 N G A 176.7 31.936 30 DPGP_VECTAGS_1-0002 12 N G G 344.5 48.0068 30 DPGP_VECTAGS_1-0002 12 N G T 478.8 61.0808 30 DPGP_VECTAGS_1-0002 12 N G C 344.4 53.6604 30 DPGP_VECTAGS_1-0002 12 N G G 263.65 39.7596 30 DPGP_VECTAGS_1-0002 12 N G A 256.7 40.0913 30 DPGP_VECTAGS_1-0002 12 N G C 224.2 28.7221 30 DPGP_VECTAGS_1-0002 12 N G T 124.55 29.8102 30