Hi all,
I am analysing data from several RAD-seq libraries. The libraries were digested with Sbf1 and single end sequenced on an Illumina HiSeq to 200 bp.
I ran the libraries through Fastqc to screen them/get an idea of the quality. Generally the library looked fine - a little filtering and trimming needed. However the kmer profile returned a progressive enrichment in TTTTT over the reads:
After demultiplexing the individuals in the library and removing adapter sequence, this enrichment went away but then the individual kmer profiles show the following odd step-wise enrichment:
Does anyone have any idea of what could be causing this? Thanks in advance for any suggestions.
Edit: So far I have been using the Stacks process_radtags module to demultiplex/screen for adapter sequences http://creskolab.uoregon.edu/stacks/comp/process_radtags.php
