Dear all,
I'm trying to use Tophat with 8 million single-end reads of 75 bp. I set all options that concern minimum intron length to 30 (because the minimum intron length in my genome reference is 39), all other option are set to the default value:
-i 30
--min-coverage-intron 30
--min-segment-intron 30
--min-closure-intron 30
In this conditions it works until the step of "Joining segment hits", but it never passed this step. I'm still waiting since yesterday morning!!!!
Is it normal? How many times does it take?
If I test this conditions on 8 millions single-end read of 35bp it completly works in ~25 minutes.
thanks for your help
Maria
I'm trying to use Tophat with 8 million single-end reads of 75 bp. I set all options that concern minimum intron length to 30 (because the minimum intron length in my genome reference is 39), all other option are set to the default value:
-i 30
--min-coverage-intron 30
--min-segment-intron 30
--min-closure-intron 30
In this conditions it works until the step of "Joining segment hits", but it never passed this step. I'm still waiting since yesterday morning!!!!
Is it normal? How many times does it take?
If I test this conditions on 8 millions single-end read of 35bp it completly works in ~25 minutes.
thanks for your help
Maria
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