what happens to paired reads that do not overlap?

[yangfa1]

Hi, I understand that in the make.contigs step, paired reads that overlap will be reconstructed to make longer contigs. I am wondering what happen to those reads that do not overlap because the fragments are too long? Are they included in output fasta file or throw away?
Thanks.

[pschloss]

See my response to a similar question that was recently asked:

make.contigs, no scrap

Hello community! I am following MiSeq SOP I am doing a run and while i am waiting for my alignment to be complete, I am rechecking and further investigating on how does mothur works. Wo I was wondering… After my make.contigs, there is nothing in my scrap file. The sequencing center said I had a good run, but I find this supcicious. yes, my reads do not fully overlaps… i should have check the forum before doing the run as recommanded by a collaborator but what is done is done anyway, as i …