I'm trying to align small groups of RNA-Seq reads within a larger FASTQ file. I need a separate alignment for each group. I can separate the read groups with an ID number or something similar, but it's not feasible to separate the groups into their own files, since there are around 10^6. I only have one reference sequence I'm trying to align to, and there isn't any alternative splicing.
Is there something that I can use for this? I've looked at the manuals for EMBOSS and Clustal O, but they don't seem to have anything appropriate. BWA has the option "-R" for setting the read group id, but I think that's just for output.
Thanks in advance for any help.