This is regarding RNA-SeQC result clarification.
when gencode.v7.annotation.gtf was used with command
java -jar RNA-SeQC_v1.1.8.jar -n 84408 -s "DGL1094|DGL-finalsort-104.bam|DGL1094" -t gencode.v7.annotation.gtf -r hg19_.fasta -o ./DGLfinalsort/ -strat gc -gc gencode.v7.gc.txt -BWArRNA human_all_rRNA.fasta -noDoC -singleEnd -transcriptDetails -rRNAdSampleTarget 1 million
thre was no rRNA count in my bam file but when used command
java -jar RNA-SeQC_v1.1.8.jar -n 84408 -s "DGL1094|DGL-finalsort-104.bam|DGL1094" -t gencode.v7.annotation.gtf -r hg19_.fasta -o ./DGLfinalsort/ -strat gc -gc gencode.v7.gc.txt -noDoC -singleEnd -transcriptDetails -rRNAdSampleTarget 1 million
rRNA count was 39462. i want to clarify is the problem with human_all_rRNA.fasta file(downloaded from webpage).
if the gencode.v19.annotation.gtf of hg 19 version was used the rRNA count was different 4506. i just want to clarify wht went wrong?
which gtf file to consider for calculation.
Hope to hear frm you
Thank you