Using the galaxy website, I used the FASTQ groomer on my Illumina RNAseq FASTQ file to convert it to a Sanger FASTQ. When doing the FASTQC on the output file, all the reads were in the lower red, poor quality range. However, if I perform FASTQC on the original illumina FASTQ, they are all in the upper green, high quality range. Is there a reason for this, and a way to avoid it?
Thanks.
Thanks.
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