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
there 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 hg19 version was used the rRNA count was different 4506. I just want to clarify what went wrong? Which gtf file to consider for calculation?
Hope to hear from you
Thank you
•
written
by
gskbioinfo143 •
1 answer
According to the manual using -BWArRNA is more robust method.
If you would like to know about rRNA reads, you could:
- Pull out the rRNA coordinates from the GTF file in a bed format and see how many reads mapped to those regions? See their mapping quality stats etc.
- Align the reads to
human_all_rRNA.fastaand see how many reads mapped there ? This should not take long time.
This is what the tool is doing but if you do independently it will give more insights to the problem.
•
written
by
GouthamAtla
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