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Old 08-02-2016, 07:13 AM   #3
dovah
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Location: Russia

Join Date: Jul 2014
Posts: 18
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Hi asier,

many thanks for your answer. I will try again the default samtools sort option, will let you know.

To answer your questions:
* The organism is D. melanogaster
* My bam files are about 33 GB each. Yes, I've been told that's pretty big, but keep in mind I had 251929648 reads (x2 because of paired-end) that survived after trimming.
* The overall RAM of the server I am using is about 60GB. I expect it to be okay to handle a sort job

And thanks for reminding me of the magical Hisat2 option, maybe this is exactly what I am missing. So actually sou are suggesting that if I add this option when Hisat2 is generating the mapping file, I will still need to sort the input bam but it will have the necessary attributes to be processed by Cufflinks?

Keeping you updated.
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