ASE-TIGAR is software to estimate the allele-specific expression (ASE) from RNA-Seq data with diploid genomes.
./merge_pat_mat_fasta.pl NA12878_pat_refMrna.fa NA12878_mat_refMrna.fa > NA12878_pat_mat_refMrna.fa
bowtie2-build NA12878_pat_mat_refMrna.fa NA12878_pat_mat_refMrna
For single-end data:
bowtie2 -p 8 -X 1000 -k 100 --very-sensitive NA12878_pat_mat_refMrna sample.fastq > sample.sam
For paired-end data:
bowtie2 -p 8 -X 1000 -k 100 --very-sensitive NA12878_pat_mat_refMrna -1 sample_1.fastq -2 sample_2.fastq > sample.sam
For single-end data:
java -jar ASE-TIGAR.jar --thread_num 8 NA12878_pat_mat_refMrna.fa sample.sam --alpha_zero 0.1 sample_out.txt
For paired-end data:
java -jar ASE-TIGAR.jar --thread_num 8 NA12878_pat_mat_refMrna.fa sample.sam --is_paired --alpha_zero 0.1 sample_out.txt
ID: transcript (mRNA) ID that the program predicted
LENGTH: transcript length
Z: the number of expected fragments that the program assigned to the transcript
FPKM: normalized expression level (Fragments Per Kilobase of exon per Million mapped fragments)
THETA: estimated parameter (transcript abundance), essentially Z divided by total mapped reads.
You can visualize the optimized alignment by ASE-TIGAR as follows:
samtools sort sample_out.txt.opt.bam sample_opt_sorted
samtools index sample_opt_sorted.bam
Please start IGV_2.3.14 or later, and load refMrna.fa as Genome, and sample_opt_sorted.bam. You can look at the optimized alignment of reads on each transcript isoform.
Any published works where ASE-TIGAR has been used in data analysis should include a citation:
Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yosuke Kawai and Masao Nagasaki A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes. accepted.
ASE-TIGAR, (c) 2015, Tohoku University (the "Software")
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