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bowtie2  -x /share/data/umw_biocore/dnext_data/genome_data_other/tRAX/hg19/db-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 1 --un ./SRR029131.unmapped.fastq  -U SRR029131_trimmed.fastq.gz | /share/data/umw_biocore/dnext_data/genome_data_other/tRAX/tRAX/choosemappings.py /share/data/umw_biocore/dnext_data/genome_data_other/tRAX/hg19/db-trnatable.txt --progname=TRAX --fqname=SRR029131_trimmed.fastq.gz --expname=TestSamples.txt --minnontrnasize=20 | samtools sort -T /tmp/SRR029131temp - -o ./SRR029131.bam
1000000 reads; of these:
  1000000 (100.00%) were unpaired; of these:
    529823 (52.98%) aligned 0 times
    280989 (28.10%) aligned exactly 1 time
    189188 (18.92%) aligned >1 times
47.02% overall alignment rate
tRNA Reads with multiple transcripts:3114
tRNA Reads with multiple anticodons:584
tRNA Reads with multiple aminos:88
Total tRNA Reads:4354
Single mapped non-tRNAs:293236
Multiply mapped non-tRNAs:168486
Imperfect matches:4249/4354