#!/bin/bash

# Use TopHat 1.0.12 to align reads from RNAseq_LPS (only reads 35bp long
# and no more than two bases with phred < 20) against sscrofa 9.56 + human rDNA


#----------------------[ Add bowtie and tophat to PATH ]-----------------------
# Uncomment as necessary
PATH=$PATH:/exports/work/vet_roslin_nextgen/dario/bowtie/bowtie-0.11.3/
PATH=$PATH:/exports/work/vet_roslin_nextgen/dario/tophat/current/bin/

tophat \
  --output-dir /exports/work/vet_roslin_nextgen/dario/tophat/output/20100114_RNAseq_LPS/ \
  --mate-inner-dist 130 \
  --mate-std-dev 30 \
  --min-anchor-length 6 \
  --splice-mismatches 0 \
  --solexa1.3-quals \
  --segment-length 35 \
  --max-multihits 10 \
  --max-intron-length 50000 \
  /exports/work/vet_roslin_nextgen/dario/bowtie/current/indexes/Sscrofa9.56_plus_Human_ribosomal_DNA_complete_repeating_unit \
  /exports/work/vet_roslin_nextgen/dario/fastq/20091217_RNAseq_AM_LPS_CTRL/filtered_35bp_phred20/RNAseq_LPS_1_35bp.fastq \
  /exports/work/vet_roslin_nextgen/dario/fastq/20091217_RNAseq_AM_LPS_CTRL/filtered_35bp_phred20/RNAseq_LPS_2_35bp.fastq \
  