Hello All
Sorry this one's a bit long
Have come here after some testing !!
I am trying to run Tuxedo suite for RNASeq Analysis on AWS
Post alignment using Tophat, I have recorded significant difference in size of "accepted_hits.bam" between runs on AWS (Amazon Web Services) and Local System
Details
Paired end FastQs
Size - after Adapter and quality thresholding - 7 gigs (3.5 X 2)
Human Sample
AWS Instance
15 cores - of - m4.16xlarge (64 cores/256 RAM)
Time ~45 min
Out put accepted_hits.bam ~100mb
Local Server
15 cores - of - 36 cores/256 RAM
Time ~52 min
Out put accepted_hits.bam ~1.2GB
Questions
Why such significant difference? reasons?
One thread I found, which was somewhat related
As suggested in the above thread, I have tried running tophat, with same parameters and input files,
on 1, 5, 10, 15, 20, 30 and 64 cores on local servers
on 30 and 64 cores on AWS
Interestingly, the size of "accepted_hits.bam" remained same (1.2 gb) till I reached 30 cores on local server (with specs mentioned above), and reduced (~120 mb) on 64 cores.
On AWS, as said above, 30 and (later) 64 are giving out ~100 mb of accepted_hits.bam
any input, suggestions and comments are welcome
thank you for your time !!
Sorry this one's a bit long
Have come here after some testing !!
I am trying to run Tuxedo suite for RNASeq Analysis on AWS
Post alignment using Tophat, I have recorded significant difference in size of "accepted_hits.bam" between runs on AWS (Amazon Web Services) and Local System
Details
Paired end FastQs
Size - after Adapter and quality thresholding - 7 gigs (3.5 X 2)
Human Sample
AWS Instance
15 cores - of - m4.16xlarge (64 cores/256 RAM)
Time ~45 min
Out put accepted_hits.bam ~100mb
Local Server
15 cores - of - 36 cores/256 RAM
Time ~52 min
Out put accepted_hits.bam ~1.2GB
Questions
Why such significant difference? reasons?
One thread I found, which was somewhat related
As suggested in the above thread, I have tried running tophat, with same parameters and input files,
on 1, 5, 10, 15, 20, 30 and 64 cores on local servers
on 30 and 64 cores on AWS
Interestingly, the size of "accepted_hits.bam" remained same (1.2 gb) till I reached 30 cores on local server (with specs mentioned above), and reduced (~120 mb) on 64 cores.
On AWS, as said above, 30 and (later) 64 are giving out ~100 mb of accepted_hits.bam
any input, suggestions and comments are welcome
thank you for your time !!
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