usage.txt

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# command line to generate allele specific transcripts
cd .
## prepare vcf file
/usr/local/tabix/latest/bin/bgzip   xxx.vcf
/usr/local/tabix/latest/bin/tabix -p vcf xxx.vcf.gz

## get transcripts
perl get_allele_specific_transcripts.pl --gff  <gff>  --genomefile <genome>  --vcf <vcf>  --out <out>
#  vcf --> vcf data of hybrid sample
# genome --> reference genome fasta file used to generate vcf file
# this script requires Vcf.pm


## get gene list file
perl get_geneID.pl --gff  <gff>  --out <out>


## The two files can be used for RSEM pipeline


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# DEMO command line for RSEM
cd RSEM
/usr/local/rsem/latest/rsem-prepare-reference  \
            --transcript-to-gene-map P1979_gene_list.txt  \
                       --bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \
                       P1979_allele_trans.fasta  ref/P1979_allele_ref &


/usr/local/rsem/latest/rsem-calculate-expression -p 5 --paired-end   \
 --bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/   \
 --estimate-rspd     --bowtie2-mismatch-rate 0.2   \
  RNAseq_R1.fq RNAseq_R2.fq  \
  ref/P1979_allele_ref   exp/RNAseq_s1