Entering edit mode
5.0 years ago
hallsalina
▴
20
I was wondering if anyone could help me with this. I need to run the picard command CollectRnaSeqMetrics below
java -jar picard.jar CollectRnaSeqMetrics \
I=input.bam \
O=output.RNA_Metrics \
REF_FLAT=ref_flat.txt \
STRAND=SECOND_READ_TRANSCRIPTION_STRAND \
RIBOSOMAL_INTERVALS=ribosomal.interval_list
and I need to create the interval_list for hg38. Is there a list I can download or if I need to create this, could someone kindly advice/guide?
Thanking you in advance!
Thank you @Dan! Works perfect!
Hi I also need a intervalist for hg38 for the picard CollectRnaSeqMetrics. Does this list also contain the 5.8S rRNA?