the lack of a file

[chyr03]

Hi,
The count data of my bam files was produced by QoRT , but the "QC.spliceJunctionAndExonCounts.withNovel.forJunctionSeq.txt.gz" file can not be founded in the outputdata directory. How does it come about? thanks for an answer.

[hartleys]

See the JunctionSeq manual, section 4.4.

In order to add the novel splice junctions, you need to run an additional QoRTs utility, "mergeNovelSplices".