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#!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
gunzip -c reads2.right.fq.gz > reads2.right.fq
fi
if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
gunzip -c reads2.left.fq.gz > reads2.left.fq
fi
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4 --no_cleanup --normalize_reads
##### Done Running Trinity #####
if [ ! $* ]; then
exit 0
fi
###########################################
# use RSEM to estimate read abundance ####
###########################################
sleep 2
# first try RSEM
../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir RSEM_outdir
# try eXpress
../../util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --seqType fq --left reads.left.fq --right reads.right.fq --SS_lib_type RF --est_method eXpress --aln_method bowtie2 --trinity_mode --prep_reference --output_dir eXpress_outdir
#######################################
## run bowtie PE to get alignment stats
#######################################
../../util/bowtie_PE_separate_then_join.pl --seqType fq --left reads.left.fq --right reads.right.fq --target trinity_out_dir/Trinity.fasta --aligner bowtie
../../util/SAM_nameSorted_to_uniq_count_stats.pl bowtie_out/bowtie_out.nameSorted.bam
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