I'm doing a metagenomic analysis on human samples that were sequenced by Miseq platform, paired end reads, 40 to 300pb long (it varies according to FastQC report). After the trim/quality control fase, i ended up with reads of 60 to 190 bp long, but those paired end reads aren't able to join anymore. :(
I thought about 2 solutions:
- Consider all reads (R1 and R2) single end reads, concatenate them all and proceed with the metagenomic analysis with QIIME, or;
- Use only forward (R1) or reverse (R2) reads for the downstream analysis with QIIME.
Is there a 3th and better option for it? Does any of the solutions i thought about make sense?
Thank you all very much for any help or tips you can provide me.