Deciding Which Version Of Tophat To Use

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11.7 years ago

narges ▴ 210

Hi all,

My dataset read length is 36 and I want to decide which version of tophat should I use. Is it correct that when the read length is less than 50 I should use the Bowtie 1 index and tophat 1 ? or can use the latest version of them as well?

many thanks in advance

tophat • 1.4k views

ADD COMMENT • link 11.7 years ago by narges ▴ 210

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which type of data ? paired-end ? illumina ? poly-A ? small RNA ?

ADD REPLY • link 11.7 years ago by Nicolas Rosewick 11k

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actually it is illumina dataset And we were thinking is it always good idea that we use the latest version of methods like here the Bowtie 2 index version or would it be more reliable that we decide about the version depending on our dataset.

ADD REPLY • link 11.7 years ago by narges ▴ 210

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and I forgot to say that there are two datasets, one paired end and one singe end.

ADD REPLY • link 11.7 years ago by narges ▴ 210

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for 36 nucleotides I would use the version 1, and remember to change the parameter that would split your read in n-mers

ADD REPLY • link 11.7 years ago by Lorena Pantano ▴ 380

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once you hone in on the problem could you please also add that as an answer - it helps when people look up questions later on, thanks

ADD REPLY • link 11.7 years ago by Istvan Albert 100k

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so do you agree with the trend that for reads shorter than 50 version 1 is ,ore efficient or are there other parameters I should take into account?

ADD REPLY • link 11.7 years ago by narges ▴ 210

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