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?
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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.Last edited by Brian Bushnell; 02-04-2015, 10:01 AM.
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