How to merge multiple sequencing runs

[vinay052003]

I have multiple fastq files generated by sequencing single end library on multiple lanes on Illumina GA. I am not sure how to merge them to generate a consolidate reference genome alignment file using Tophat.
If I had multiple fastq files for paired end reads, I would have run TopHat by providing two comma separated lists of files to TopHat. But I am not sure if I can do that with single end reads as well.
Any thoughts?


Thanks.

[adaptivegenome]

You can map each fastq separately and merge the BAMs with samtools.

[westerman]

You should also just be able to 'cat' the files together into one large file.

[jbrwn]

map them all as individuals in tophat, then use samtools merge to put them together.

[pbluescript]

I would first map them all separately as others have suggested and then calculate RPKMs for each sample. Compare the RPKMs between the samples, and if they all look similar, you can be reasonably sure there are no lane issues with your run. After that, I would use the cat command to combine the fastq files and then rerun the mapping with the combined file.