Hi everybody !
I want to annotate a non-model organism genome.
I am using (among other) 454 RNA-seq single-end reads.
I read several topics about the mapping of 454 RNA seq but they are quite old...
It seemed that using TopHat was not OK because TopHat can deal only with short reads (like Illumina)
However, now there is TopHat2 using Bowtie2.
Apparently, they can deal with longer reads : In the manual (http://tophat.cbcb.umd.edu/manual.shtml), it is written : TopHat can align reads that are up to 1024 bp long.
What do you think ?
Is it now OK to align 454 reads with TopHat ?
If yes, do you have any recommendation concerning the parameters to use ?
Thanks a lot !
Muriel
I want to annotate a non-model organism genome.
I am using (among other) 454 RNA-seq single-end reads.
I read several topics about the mapping of 454 RNA seq but they are quite old...
It seemed that using TopHat was not OK because TopHat can deal only with short reads (like Illumina)
However, now there is TopHat2 using Bowtie2.
Apparently, they can deal with longer reads : In the manual (http://tophat.cbcb.umd.edu/manual.shtml), it is written : TopHat can align reads that are up to 1024 bp long.
What do you think ?
Is it now OK to align 454 reads with TopHat ?
If yes, do you have any recommendation concerning the parameters to use ?
Thanks a lot !
Muriel
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