i) Identfication of ASIs:

• Given the CCS reads of the single-molecule RNA-Seq: sample_raw.longReads.fasta;

             the high-quality isoform assembled using IsoSeq: sample_hq_isoform.fastq;

             NGS RNA-Seq reads: sample_NGS.reads.fasta;

             Reference genome: ref.fa

• Mapping the CCS reads to reference genome with GMAP and minIntronLength = 25 nt, generating SAM file: sample_raw.longReads.sam
• ./transcriptIdentify sample_raw.longReads.sam >sample_transcripts.txt
• ./pseudoReadRefCoord sample_transcripts.txt >sample_pseudo.longReads.coord.txt
• ./pseudoReadsSeqExt ref.fa sample_pseudo.longReads.coord.txt >sample_pseudo.longReads.fasta
• ./rawReadSeqModify sample_transcripts.txt sample_raw.longReads.fasta >sample_modified.longReads.fasta

• Mapping 'sample_NGS.reads.fasta' against 'sample_pseudo.longReads.fasta';

  Recalling SNPs with SAMtools, generating BCF-derived VCF file: sample_bcf.txt;

  Low-quality filtering of 'sample_bcf.txt', generating: sample_filtered.vcf.txt

• ./bcfCorrect sample_bcf.txt sample_pseudo.longReads.fasta >sample_NGS.corrected.pseudo.longReads.fasta
• ./lqMark sample_vcf.txt sample_NGS.corrected.pseudo.longReads.fasta >sample_lq_marked.NGS_corrected.pseudo.longReads.fasta
• ./snpMark sample_vcf.txt sample_lq_marked.NGS_corrected.pseudo.longReads.fasta >sample_SNP_marked.NGS_corrected.pseudo.longReads.fasta

• ./modifiedLongReadsCorrect sample_pseudo.longReads.coord.txt sample_modified.longReads.fasta sample_filtered.vcf.txt sample_SNP_marked.NGS_corrected.pseudo.longReads.fasta

  #Automatically generating two files: SNP_marked.NGS_corrected.modified.longReads.fasta; modified.longReads.SNP.annotation.txt;

  Renaming the files with 'sample_SNP_marked.NGS_corrected.modified.longReads.fasta' and 'sample_modified.longReads.SNP.annotation.txt'

• ./snpSet sample_pseudo.longReads.coord.txt sample_filtered.vcf.txt

  #Automatically generating a file: chr_index_SNP.txt;

  Renaming the file with 'sample_chr_index_SNP.txt'

• ./phasing sample_modified.longReads.SNP.annotation.txt sample_chr_index_SNP sample_SNP_marked.NGS_corrected.modified.longReads.fasta

  #Automatically generating 9 files:
       (1) to_be_phased.txt ;
       (2) to_be_phased_2.txt;
       (3) to_be_phased_2_ann.txt;
       (4) to_be_phased_2_stat.txt;
       (5) phased_raw.txt;
       (6) phased_correction.txt;
       (7) read_phased.txt;
       (8) corrected.modified.longReads.fasta;
       (9) phased.modified.longReads.fasta;
  

  Renaming the files with a prefix 'sample_' added.

ii) Quantification of ASIs:

• Mapping 'sample_hq_isoform.fastq' to reference genome with GMAP, generating SAM file: sample_hq_isoform.sam
• ./transcriptIdentify sample_hq_isoform.sam >sample_hq_isoform_transcripts.txt

• ./phasedIso sample_chr_index_SNP.txt sample_hq_isoform.fastq sample_phased_raw.txt sample_hq_isoform_transcripts.txt

  #Automatically generating 2 files:，isoform_phased.txt; phased.hq_isoform.fasta;

  Renaming the files with 'sample_isoform_phased.txt' and 'sample_phased.hq_isoform.fasta' resepctively

• Mapping 'sample_NGS.reads.fasta' against 'sample_hq_isoform.fastq' with bowtie or bwa, reporting at most 2 best matches, generating SAM file: sample_ngs.hq_isoform.sam
• ./asiqFilt sample_ngs.hq_isoform.sam >sample_ngs.hq_isoform.filtered.sam
• ./asiq sample_isoform_phased.txt sample_ngs.hq_isoform.filtered.sam >sample_asiq.out.txt