Forward and Reverse Reads Out of Order

Question

[dw845316]

Hello Friends,

I have amplicon Miseq data that I have parsed using the amplification primers. My issue now is that the forward and reverse parsed gene files are no longer in the same order. Qiime requires forward and reverse fastq files to be in the same order(based on read-ID). I need a script or program to create one forward and one reverse fastq file that contains reads in the same order, and only contains reads that were found in both the forward and reverse files.

Thanks,

Danny

Answer 1

[h.mon]

Try repair.sh from the BBTools / BBMap suite:

repair.sh in1=broken1.fq in2=broken2 out1=fixed1.fq out2=fixed2.fq outs=singletons.fq repair

Read the guide and pay attention to memory usage. Depending on how much your files have been messed up, it may be worth starting over, this time processing paired files with programs that do not mess them.