Steps of the AW pipeline and Java processing.

1Raw read files (.fastq), GS (genome sequence, fasta), annotation file (.gtf), alignment file (.bam), variant file (.vcf), SNP coverage (.bed), transcript counts (.xprs).
2Though not listed in their output column, all scripts output an.html summary file. The two Java build programs enter summary information into their database for display by their Java query program.
3Pipeline scripts are Perl, except QC is shell. Each script executes one or more tools on all input files, renames the result files with their library abbreviations, puts them into the/Results directory, and writes the summary.html file.
4These steps are only necessary if the variant file is not available.
5runAW must be executed before the “Transcripts counts” step to produce the parental transcript files and again afterwards to update the database with the transcripts heterozygous count files. The optional AW build files are not needed for the initial build.
6Java graphical interface.
Steps of the AW pipeline and Java processing.