Hellow
I have got Roche/454 RNA-Seq reads from human samples.
It seems that TopHat/Cufflinks is one of the most used pipeline for analyzing RNA-Seq data, however, for short reads only (non-454 reads).
The program Bowtie, which is called by TopHat, cannot map 454 reads.
Still I would like to take adavantage of TopHat's features if possible.
Has anybody tried to use 454 reads with TopHat, implemented a workaround, or are there any alternatives to TopHat/Bowtie that yield good results for 454 reads?
Any help, comments are appreciated!
I have got Roche/454 RNA-Seq reads from human samples.
It seems that TopHat/Cufflinks is one of the most used pipeline for analyzing RNA-Seq data, however, for short reads only (non-454 reads).
The program Bowtie, which is called by TopHat, cannot map 454 reads.
Still I would like to take adavantage of TopHat's features if possible.
Has anybody tried to use 454 reads with TopHat, implemented a workaround, or are there any alternatives to TopHat/Bowtie that yield good results for 454 reads?
Any help, comments are appreciated!
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