I am having trouble to demultiplex and trim primers and barcodes from a fastq paired-end file.
I have one single pair of fastq file from a paired-end MiSeq run and an oligo file like this:
primer AYTGGGYDTAAAGNG CCGTCAATTYHTTTRAGT V4 primer CCGTCAATTYHTTTRAGT AYTGGGYDTAAAGNG V5 BARCODE ACCTGATCCGCA ACCTGATCCGCA NOD_1 BARCODE GTTGACCATCGC GTTGACCATCGC NOD_2 BARCODE TGACTGCGTTAG TGACTGCGTTAG NOD_3
I used this command:
make.contigs(file=stability.files, oligos=pool94.oligos,bdiffs=1, processors=8)
However, I get 99.99% of the reads on the scrap file without trimming or any information of each detected sample.
My groups file looks like:
M00430_5358_000000000-CCGRN_1_1101_10216_15499 pool94 M00430_5358_000000000-CCGRN_1_1101_10594_20693 pool94 M00430_5358_000000000-CCGRN_1_1101_10676_10175 pool94 M00430_5358_000000000-CCGRN_1_1101_10878_13512 pool94 M00430_5358_000000000-CCGRN_1_1101_11087_21332 pool94 M00430_5358_000000000-CCGRN_1_1101_12496_11697 pool94 M00430_5358_000000000-CCGRN_1_1101_12859_24247 pool94
My question is, can mothur detect the barcode and primers anywhere on the read? or is it expecting it to be at the beginning of the read?
My Reads look like this:
The first match is the bc and the second the primer:
Thanks for your attention.
Can someone clarify it to me?