Hello, totally new to the forum and somewhat new to the sequencing world. I've dealt with miseq data before when it arrives in the "standard" forward/reverse fastq reads with or without primers. I then go straight into PANDAseq, USEARCH8, and QIIME then process the outputs in R and I'm fairly comfortable with all of that.
My recent probelm comes from a large project that is using JGI for sequencing (miseq), which gives you data in a non-standard format. Does anyone have experience dealing with this to get me to the point I'm more familiar with. I've already figured out how to split the forward and reverse reads and extract barcodes but am having troubble with the quality filtering and trimming as well as the naming of the files. I'll be putting a large number of samples through this pipeline that will eventually have reused barcodes so any advice on renaming files is also appreciated.
Thanks in advance for the help and I look forward to hearing peoples suggestions!
My recent probelm comes from a large project that is using JGI for sequencing (miseq), which gives you data in a non-standard format. Does anyone have experience dealing with this to get me to the point I'm more familiar with. I've already figured out how to split the forward and reverse reads and extract barcodes but am having troubble with the quality filtering and trimming as well as the naming of the files. I'll be putting a large number of samples through this pipeline that will eventually have reused barcodes so any advice on renaming files is also appreciated.
Thanks in advance for the help and I look forward to hearing peoples suggestions!
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