Jumping library and regular fragment library

[foxyg]

If I have a sample sequenced using both Jumping library and fragment library, can I combine the fastq files? Are there any reason I should not do this?

Thanks

[Brian Bushnell]

There are lots of reasons to not do this. They almost certainly have different adapter types which need to be trimmed differently. They may have different orientations, as well. And I assume you are using them for assembly... it depends on the assembler, but many use the long jump libraries for scaffolding and work best if a given library has a consistent insert size.

After any preprocessing you do, though, if you are just doing a basic DeBruijn assembly with no scaffolding, there's nothing wrong with lumping them together for the purpose of building kmer count tables.