Question: SGFeatureCounts function in SGSeq package failed to generate splice graphs
0
gravatar for mgdrnl
22 months ago by
mgdrnl0
mgdrnl0 wrote:

Hello

I think this question is for the package developers, but maybe somebody had the same problem. I am traying to analyze 59 bam files in a computer with 110GB of available memory usage, all bam files occupy 149GB. I can't obtain the splice graph and I don't get any error message.. I monitorized the process and it looks like the memory is full for this process, so maybe that is the reason. I parallelize the process with 12 CPU, but still it is not enough. To obtain the SGFeatureCounts class, all bam files are downloaded to R first? If it is so, I guess I would need to increase the memory.. Could you give me any advice how can I complete the process in my computer?

Thank you,

Magda

sgseq • 267 views
ADD COMMENTlink modified 22 months ago by Leonard Goldstein80 • written 22 months ago by mgdrnl0
Answer: SGFeatureCounts function in SGSeq package failed to generate splice graphs
0
gravatar for Leonard Goldstein
22 months ago by
United States
Leonard Goldstein80 wrote:

Hi Magda,

Can you please provide more details -- what commands were used to generate the SGFeatureCounts object and what package versions were used i.e. output of sessionInfo(). For larger analyses I strongly recommend not to use wrapper functions like analyzeFeatures() and instead run individual analysis steps separately (see section 12 of the vignette). This helps with troubleshooting and allows saving and inspecting of intermediate results. Please also see section 13 for recommendations on using multiple cores and typical memory requirements. 

Leonard

ADD COMMENTlink written 22 months ago by Leonard Goldstein80
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 221 users visited in the last hour