bunzip2 -df /projects/NBL/HS1803/616GYAAXX_5/tophat_wj/616GYAAXX_5_1_concat_qseq.txt.bz2 ...
bunzip2 -df /projects/NBL/HS1803/616GYAAXX_5/tophat_wj/616GYAAXX_5_2_concat_qseq.txt.bz2 ...
Filtering Reads: False
lc==1000000
lc==2000000
lc==3000000
lc==4000000
lc==5000000
lc==6000000
lc==7000000
lc==8000000
lc==9000000
lc==10000000
lc==11000000
lc==12000000
lc==13000000
lc==14000000
lc==15000000
lc==16000000
lc==17000000
lc==18000000
lc==19000000
lc==20000000
lc==21000000
lc==22000000
reads included: 22806670
reads excluded: 0

Filtering Reads: False
lc==1000000
lc==2000000
lc==3000000
lc==4000000
lc==5000000
lc==6000000
lc==7000000
lc==8000000
lc==9000000
lc==10000000
lc==11000000
lc==12000000
lc==13000000
lc==14000000
lc==15000000
lc==16000000
lc==17000000
lc==18000000
lc==19000000
lc==20000000
lc==21000000
lc==22000000
reads included: 22806670
reads excluded: 0

/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat -r 245 -o /projects/NBL/HS1803/616GYAAXX_5/tophat_wj -G /projects/NBL/reference_files/UCSC/all.gtf.gff3 /projects/rcorbettprj/trans_abyss/bowtie_index/hg18 /projects/NBL/HS1803/616GYAAXX_5/tophat_wj/616GYAAXX_5_1.fastq /projects/NBL/HS1803/616GYAAXX_5/tophat_wj/616GYAAXX_5_2.fastq ...