Closed pchamely1 closed 5 years ago
Hey Chris,
After much googling, I realized that there limits to the amount of memory that can be used by all of your R objects and since my fastq files were so large I figured this was the issue. I was able to get the MULTIseq.preProcess step to work with my fastq's by submitting the script as a job to the cluster or running the script during an interactive qlogin session!
Best, Paulina
Hi Chris,
I'm trying to use your deMULTIplex tool to demultiplex my hashed single cell data but it seems to keep terminating at the MULTIseq.preProcess step. I realized that the issue is with the ShortRead function readFastq( ). I think my fastq may just be too big (it has ~13mil reads) as readFastq() runs fine when I split my fastq into 4 subfiles (of ~3mil reads each). Do you think this is the real issue and if yes, how do I go about creating one readTable, incorporating all of the information in the full fastq, without having to create 4 seprate readTables and merging them after.
Thanks, Paulina