I am working on ribosome profiling - I downloaded, trimmed and aligned reads to rRNA using bowtie2, then took the unmapped reads and aligned them to the ucsc_hg19 reference with the hg19 gtf using TopHat2.
The thing is - there is a very low alignment rate (only 3498 reads were aligned).
Which makes me think I did something wrong...
I did a check with BWA mem to see if the rates are better - and they are much much higher. The cmd. is:
/nadata/software/tophat-2.0.12.Linux_x86_64/tophat2 -G ucsc_hg19.gtf -o ./ribo_bam -M -p 3 --no-novel-juncs -g 5 ./ucsc_hg19 4TopHat_reads.fastq
Can anyone tell me what I'm missing?