The package contains:
- Pipeline specific to F1 hybrid (inbred) RNA-seq data.
- Input: RNA-seq from one or more libraries (optional replicas), the genome sequence to align to, the gene annotation file,
and an optional VCF variant file.
- Output: The heterozygous SNPs. Optionally, it can also output the VCF file and
transcript heterozygous read counts.
- runAW is a Java interface to build the MySQL database.
- Input: the gene annotation file, genome sequence, VCF file and heterozygous SNP file. Optionally, it can take as input variant effects, NCBI annotation and transcript heterozygous read counts.
- Compute: Allele Imbalance (AI) is computed for both the heterozygous SNP coverage and heterozygous
transcript read counts. If effects are not loaded, a subset are computed. The parental spliced transcripts
and protein sequences are computed. Other various supporting information and summary statistics.
- Output: the AW database along with files of the parental spliced transcripts and protein sequences.
- viewAW is a Java interface to view the database.
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