bunzip2 -df /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_1_export.txt.bz2 ...
bunzip2 -df /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_2_export.txt.bz2 ...
/home/pubseq/BioSw/Maq/maq-0.7.1_x86_64-linux/scripts/fq_all2std.pl export2std /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_1_export.txt > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_1_export.txt.fastq
/home/pubseq/BioSw/Maq/maq-0.7.1_x86_64-linux/scripts/fq_all2std.pl export2std /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_2_export.txt > /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_2_export.txt.fastq
/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat -r 526 -o /projects/NBL/HS1194/311L9AAXX_3/tophat_wj -G /projects/NBL/reference_files/UCSC/all.gtf.gff3 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_1_export.txt.fastq /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/311L9AAXX_3_2_export.txt.fastq ...