Deciding Which Version Of Tophat To Use
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
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
TOPHAT error in mapping left_kept_reads step during a mapping with fusion search with bowtie1
written by Gabriel Wajnberg
-
Tophat err =1
written by Harumi •
-
RNA seq NGS data analysis
written by poonam.bi01 •
-
failed to transcriptom indexing with tophat2
written by zizigolu
-
Error Happened When Using Tophat To Run On The One-End Of Paired-End Rna-Seq Data
written by zhouchan99 •
-
Consistency Between Bowtie, Tophat And Cufflinks Versions
written by narges •
-
Tophat : Read Length Warning
written by narges •
-
Running Tophat Over Multiple Files
written by narges •
-
Recount Website Public Datasets
written by narges •
-
Tophat Question: No Accepted_Hits.Bam Generated
written by Rnaer •
which type of data ? paired-end ? illumina ? poly-A ? small RNA ?
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.
and I forgot to say that there are two datasets, one paired end and one singe end.
for 36 nucleotides I would use the version 1, and remember to change the parameter that would split your read in n-mers
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?
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