Issues with the MULTIseq.preProcess step

[pchamely1]

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

[pchamely1]

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