Howdy RNA seq files are quite large ca. 2 gbytes fastq compressed. Paired end. I’ve used rnastar. Tried to map to hg38 used whole used whole human genome annotation gtf file from ucsf genome browser. Average read size 124 bp, average fragment size 450 bp. For rnastar junction overlap used 111 bp.
These are results from log file. Looks like a lot of the reads were unmapped? I got a similar result from top hat.
2 3 4 N_unmapped 23359811 23359811 23359811 N_multimapping 386274 386274 386274 N_noFeature 193779 2056977 202263 N_ambiguous 1867858 44759 1853764 uc031tla.1 0 0 0
I’m having trouble judging the quality of the alighment. I used rnastar because I heard it is supposed to be faster and just as sensitive as hisat. Qc of reads looks good. Maybe the problem is with the reference genome/gtf file.
Greatly appreciate your answers to previous questions. Mike (mbt5766)