I seem to have some contamination in my demultiplexed sequences, but I'm not sure what to make it: is it phix contamination? library prep contamination? something else? details:
gDNA from 96 eukaryotic individuals were ddRADseq prepped per Parchman et al. 2012, sequenced on one late of illumina nextseq500 with 83bp PE reads. Raw files were demultiplexed with process_radtags in STACKS:
process_radtags -P -p ./raw_reads_fastq_format/ -b ND_barcodes5.txt -o ./demultiplexed_jan_2019/ -r -i fastq -y gzfastq --inline_null --renz_1 ecoRI --renz_2 mseI -s 10 -w 0.15 --disable_rad_check -D
blasting resulting sequences hits mostly prokaryotic genomes, including phix. further, some of the files contain a low diversity of sequences. any insight would be appreciated!
gDNA from 96 eukaryotic individuals were ddRADseq prepped per Parchman et al. 2012, sequenced on one late of illumina nextseq500 with 83bp PE reads. Raw files were demultiplexed with process_radtags in STACKS:
process_radtags -P -p ./raw_reads_fastq_format/ -b ND_barcodes5.txt -o ./demultiplexed_jan_2019/ -r -i fastq -y gzfastq --inline_null --renz_1 ecoRI --renz_2 mseI -s 10 -w 0.15 --disable_rad_check -D
blasting resulting sequences hits mostly prokaryotic genomes, including phix. further, some of the files contain a low diversity of sequences. any insight would be appreciated!
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