Has anyone tried to use BAM files from the IonExpress (Life Technologies) which are mapped using the TMAP software? Just looking at the output, it seems like TMAP is not very splice aware. I read that it does use BOWTIE2 for aligning, but there is no mention of TOPHAT. Does anyone know if these files can be used for RNAseq or should I just start over from the Fastq files?
for a more thorough answer, mappers are generally not splic aware, how the deal with splice junctions depends, usually, on paramerer choices. In principle you should be able to use a bam file from tmap, however, not every bam file will work with every software (for instance, RSEM has very specific requirements). If it was me, I would probably start from the fastq files becasue it doesn't take very long and I would know exactly how the mapping was done.
Thanks, Mike. Yes, I know the mappers usually are not splice aware, that's why I asked about TMAP, because it is some proprietary product and I can't figure out if they use TOPHAT as well to construct the BAM files. All I know is it uses BOWTIE2.
In other news, our paper on the human disease genes in flies is over 200 citations now. Not bad, eh? Hope you are doing will at Purdue.
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