Hi!
I have been trying to run RNA STARsolo on each of four single cell RNA-Seq fastq files from the same experiment.
(see als: STARsolo runs out of memory on the BAM sorting step)
All of them fail to align except for one. Each one fails with an error message that says:
“EXITING because of fatal ERROR: not enough memory for BAM sorting”
A post on the STAR github site (not enough memory for BAM sorting · Issue #870 · alexdobin/STAR · GitHub) says they were able to solve the same problem by changing a sorting parameter:
You can try to increase --outBAMsortingBinsN from the default 50 to 100 or even 200, though it will require a large number of open files.
It seems like there a few loci that are very highly expressed, which STAR sorting cannot deal nicely with… So it may be a safer option to use the samtools sort.
Is there a way that I can change --outBAMsortingBinsN?
- Ann Loraine