TopHat and Fastq with different Lane numbers

Question

[kanwarjag]

I have a very naive question will TopHat handle successfully in default conditions FastQ files merged from different lanes. I get a generic error TopHat failed. What will be best approach align Fastq fro different lanes separately then merge Bam?

Any suggestion pleas

Answer 1

[WouterDeCoster]

A suggestion to narrow down the origin of your error would be to use Tophat on just one of the fastq files and see if the error reproduces or not.