which tool can be used for an alternate for Hisat2 ??

[pjyoti29]

Hello everyone,

I am following the tutorial https://github.com/griffithlab/rnaseq_tutorial/ .
Since, Hisat requires huge RAM, I am getting message "out of memory". which other splice aware aligner can be used instead, with less computer itensive algorithm.

Thanks

[ckeeling]

Hello @pjyoti29

I'm just a user of hisat2, but I don't find that hisat2 requires a lot of memory. I'm giving it 64Gb for 4 cpus, but it is only using about 10% of that during the run. Do you have an exceptionally large reference genome, or huge read files? What is your configuration?

Cheers,

Chris

[pjyoti29]

Hi.. I am using 32gb RAM and 8 CPU. But i get the error message "out of memory" or "hisat2 killed". I am not able to figure out exact reason. I am working on insect genome ~600mb size. Thanks

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On Fri, Nov 18, 2022 at 7:33 PM Chris Keeling ***@***.***> wrote: Hello @pjyoti29 <https://github.com/pjyoti29> I'm just a user of hisat2, but I don't find that hisat2 requires a lot of memory. I'm giving it 64Gb for 4 cpus, but it is only using about 10% of that during the run. Do you have an exceptionally large reference genome, or huge read files? What is your configuration? Cheers, Chris — Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANE6PSJSVKFTTHVZGBXZNATWI6EEHANCNFSM6AAAAAASELUTPA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Dr. JYOTI PATHAK Research Associate ICAR-National Bureau of Agricultural Insect Resources Hebbal, Bangalore