Hi,
I have got a fasta file that which seem to contain some overrepresented sequence bits in it. (Seems that some sequences have got adapters still clinging to them).So I thought trim.seqs should take care of removing those oligos from sequences, or will they just remove all sequences containing these oligos?
I have tried both to put those two oligos into oligo files as primers and as barcodes.
example. run 1.
pcr.seqs(fasta=IValgus.fastq.keep.below, oligos=ollikad, processors=8)
where ollikad is a file
forward GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC
forward AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATG
and run 2.
where ollikad is a file
barcode GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC TRUSEQ1
barcode AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATG TRUSEQ2
Both of the runs will result with empty trim.file and all sequences being sorted to scrap.file.
As a matter of fact the run which had these oligos tagged as barcodes, will add |b at the end of the sequence names in scrap.file not group names TRUSEQ1 or 2.
What is going on? Can I somehow still use the trim.seqs or pcr.seqs to accomplish my task? *What did I do wrong, or is there some bug?
The version information for these runs is.
64Bit Version
mothur v.1.28.0
Last updated: 11/2/2012
*The task being to remove these oligos from my sequences.