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Old 01-11-2019, 08:10 AM   #1
sjkimble
Junior Member
 
Location: West Lafayette, IN

Join Date: Apr 2012
Posts: 4
Default sample contamination?

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!
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