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#!/bin/bash -ve
if [ -e mm9chr17.fasta.gz ] && [ ! -e mm9chr17.fasta ]; then
gunzip -c mm9chr17.fasta.gz > mm9chr17.fasta
fi
if [ -e mm9chr17.annotation.bed.gz ] && [ ! -e mm9chr17.annotation.bed ]; then
gunzip -c mm9chr17.annotation.bed.gz > mm9chr17.annotation.bed
fi
if [ -e mm9chr17.tophat.bam ] && [ ! -e mm9chr17.tophat.sam ]; then
samtools view mm9chr17.tophat.bam > mm9chr17.tophat.sam
fi
../../util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM mm9chr17.tophat.sam -I 100000 --SS_lib_type RF
find Dir_mm9chr17.tophat.* -regex ".*reads" > read_files.list
../../util/support_scripts/GG_write_trinity_cmds.pl --reads_list_file read_files.list --paired --SS > trinity_GG.cmds
/usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -vv
## execute the trinity commands, and then pull together the aggregate fasta file like so:
find Dir_mm9chr17.tophat.* -name "*inity.fasta" | ../../util/GG_trinity_accession_incrementer.pl > mm9.Trinity-GG.fasta
# which will ensure that each trinity accession is unique.
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