How To Combine Multiple Indexed Files

Question

[fanx]

Hi, I am using Bowtie 2 to index a sequence file. The Bowtie has an index limt about 3 Gb in size. My sequence file is about 10 Gb and thus indexed by separating it into 4 small files (2.5 Gb each). Does anyone know the potential to combine indexed files? Thanks. fanx

Answer 1

[JC]

I think you cannot combine indexes in Bowtie (please correct me if I'm wrong), you need to do that in postprocessing the outputs, the simple way is to map the same reads against the 4 indexes and then combine the 4 outputs excluding sequences not mapped or filtering all the posibilites.

PD: a 10Gb genome? what is that? a polyploid plant?

[Istvan Albert]

As JC said you cannot possibly combine indices - that's why the limit exists in the first place. You may be able to split the genome into smaller parts and align that way - but that too leads to another set of problems. Perhaps you might look into using a different aligner - not sure what the limits of bwa are.

[fanx]

I think BWA, like Bowtie, has a limit at 3.0 Gb for the indexing.

[fanx]

JC, Thanks. It's a good idea to take care the results after the mapping. My 10 Gb sequence data is not a genome. It is simulated 454-like data to look at the extent of protocol-assosiated artificial reads.

[Arun]

fanx, I don't understand. Then what are you indexing with bowtie?