I am mapping my illumina reads on the transcriptom by bowtie2 but the rate of alignment is too LOW(0.9). When I tried my reads on genome the alignment increased 3 times. anyway I have to use transcriptome by bowtie2 (I should not use tophat), then with which option I can truncate my reads to 50 bases?
I tried this option but
bowtie2 -x CDS -N 2 -L 28 -X 50 -U SRR1688549-ribo.fastq -S SRR1688549.sam
Thank you for your help