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 using the process_radtags module of the Stacks pipeline, 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?
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 using the process_radtags module of the Stacks pipeline, 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?
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