Hi all,
I am new to the forum but excited about the wealth of knowledge available. I am working on a NGS project in Galaxy using data from an Illumina HiSeq 2000. The first part of my workflow uses the Toothbrush FASTQ Groomer to convert the raw, paired end Illumina .fastq files into .fastqsanger. Then, I use the FASTQ Summary Statistics tool and from there use the "Draw nucleotides distribution chart". The resulting chart can be seen here.
Have any of you seen anything like this? My intuition is that the problem lies with the grooming illumina to sanger step, but I am very new to the field. If there is any other information I can provide to help diagnose the problem, please let me know.
Thanks.
I am new to the forum but excited about the wealth of knowledge available. I am working on a NGS project in Galaxy using data from an Illumina HiSeq 2000. The first part of my workflow uses the Toothbrush FASTQ Groomer to convert the raw, paired end Illumina .fastq files into .fastqsanger. Then, I use the FASTQ Summary Statistics tool and from there use the "Draw nucleotides distribution chart". The resulting chart can be seen here.
Have any of you seen anything like this? My intuition is that the problem lies with the grooming illumina to sanger step, but I am very new to the field. If there is any other information I can provide to help diagnose the problem, please let me know.
Thanks.
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