I’m trying to determine the % of RNA sequencing read that have mapped to rRNA q, but keep running into trouble using theCollectRNASeqMetrics tool. I have downloaded a rRNA interval list from:http://sourceforge.net/mailarchive/message.php?msg_id=27560147
I’ve tried to use the the Bedtointerval tool to convert the file into Picard interval, but I get following error:
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/024/667/24667223/_job_tmp -Xmx7g -Xms256m
07:55:52.779 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cvmfs/main.galaxyproject.org/deps/_conda/pkgs/picard-2.18.
Anyone who can please share any experience?