I am trying to use the featureCounts function in the Rsubread (1.12.6) package in R (3.0.1). I have done this without problems before. This time I am summarizing reads for each intron, meaning my count table should have about 600000 rows for each intron feature. R keeps on crashing, giving me a segfault error.
Any ideas what I could be doing wrong? Does featureCounts run into problem when summarizing across a very large numbers of features? Did anyone successfully use featureCounts on over 500k features?