Hi there,
I'm sequencing amplicons on the MiSeq for soil metagenomics, and some of my amplicons are length variable. As a result, some are longer than 500bp. I'm faced with throwing out some of these reverse reads for ITS1 as they won't merge/ assemble.
I've thought up a scheme that might enable me to use them and I'm wondering what you think.
If I could merge them together and have a standard set of gaps in between the forward and reverse reads, then I could align them against a database to get the "proper" gap length.
I'm having trouble finding software that can do this merging, but first I want to confirm that fastq files actually provide enough information to merge reads based on sequence identifier titles without sequence overlaps.
Tophat's capabilities are the closest to what I need, but it needs a whole reference genome instead of an amplicon reference library to align against.
Thanks!
-Jeff
I'm sequencing amplicons on the MiSeq for soil metagenomics, and some of my amplicons are length variable. As a result, some are longer than 500bp. I'm faced with throwing out some of these reverse reads for ITS1 as they won't merge/ assemble.
I've thought up a scheme that might enable me to use them and I'm wondering what you think.
If I could merge them together and have a standard set of gaps in between the forward and reverse reads, then I could align them against a database to get the "proper" gap length.
I'm having trouble finding software that can do this merging, but first I want to confirm that fastq files actually provide enough information to merge reads based on sequence identifier titles without sequence overlaps.
Tophat's capabilities are the closest to what I need, but it needs a whole reference genome instead of an amplicon reference library to align against.
Thanks!
-Jeff
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