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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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Fixed (Non-Random) Seed for 'rsem-simulate-reads' #6

Closed syounkin closed 8 years ago

syounkin commented 10 years ago

My goal was to create a version of rsem-simulate-reads that uses a fixed seed. We are using the simulator for some work here at UW-Madison, but in order to ensure reproducibility we needed a way to fix the seed in rsem-simulate-reads.

I accomplished this by adding a few lines to the makefile, and creating two header files.

The header files are identical except for how they treat the seed for the random number generator.

Now, during make, rsem-simulate-reads-fixed-seed is created using the alternative header file simul-fixed-seed.h.

The file simul-random-seed.h exists as a placeholder for the original simul.h file.

Certainly there is a better way to include fixed seed functionality, but I thought you might be interested in this solution in the short term.

All simulators should have the ability to fix the seed, and I encourage you to incorporate fixed seeds into your program.

We appreciate RSEM very much, and are grateful that the source was available on Github.

I look forward to your comments.

Thanks,

Sam UW-Madison Department of Biostatistics and Medical Informatics Kendziorski Group

bli25wisc commented 10 years ago

Hi Sam,

Thanks for your suggestion and patch. I have added an option '--seed seed' to rsem-simulate-reads according to your suggestion. It will be released in the next version.

Best, Bo

On 2014-03-17 09:34, Samuel Younkin wrote:

My goal was to create a version of rsem-simulate-reads that uses a fixed seed. We are using the simulator for some work here at UW-Madison, but in order to ensure reproducibility we needed a way to fix the seed in rsem-simulate-reads.

I accomplished this by adding a few lines to the makefile, and creating two header files.

The header files are identical except for how they treat the seed for the random number generator.

Now, during make, rsem-simulate-reads-fixed-seed is created using the alternative header file simul-fixed-seed.h.

The file simul-random-seed.h exists as a placeholder for the original simul.h file.

Certainly there is a better way to include fixed seed functionality, but I thought you might be interested in this solution in the short term.

All simulators should have the ability to fix the seed, and I encourage you to incorporate fixed seeds into your program.

We appreciate RSEM very much, and are grateful that the source was available on Github.

I look forward to your comments.

Thanks,

Sam UW-Madison Department of Biostatistics and Medical Informatics

Kendziorski Group

YOU CAN MERGE THIS PULL REQUEST BY RUNNING

git pull https://github.com/syounkin/RSEM master

Or view, comment on, or merge it at:

https://github.com/bli25wisc/RSEM/pull/6 [1]

COMMIT SUMMARY

  • Created header files simul-fixed-seed.h and simul-random-seed.h
  • Edited makefile to create rsem-simulate-reads-fixed-seed
  • Created .gitignore

FILE CHANGES

  • A .gitignore 2
  • M makefile 3
  • A simul-fixed-seed.h 4
  • A simul-random-seed.h 5

PATCH LINKS:

Reply to this email directly or view it on GitHub [1].

Links:

[1] https://github.com/bli25wisc/RSEM/pull/6 [2] https://github.com/bli25wisc/RSEM/pull/6/files#diff-0 [3] https://github.com/bli25wisc/RSEM/pull/6/files#diff-1 [4] https://github.com/bli25wisc/RSEM/pull/6/files#diff-2 [5] https://github.com/bli25wisc/RSEM/pull/6/files#diff-3 [6] https://github.com/bli25wisc/RSEM/pull/6.patch [7] https://github.com/bli25wisc/RSEM/pull/6.diff