FASTQ Groomer makes data worse?

[master_shake]

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.

[master_shake]

After searching, I believe the issue is that my data is Illumina 1.9 FASTQ, which is equivalent to a Sanger input for the FastQ Groomer. I will try this and update if it worked.

[sugo]

I know you posted this quite a while ago... but did you ever figure out what was wrong? I am having the exact same problem - I tried to run my reads through CLIP, and it told me they were the wrong quality format. So I ran them through groomer, and got these terrible scores. And when the raw reads are run through FastQC, it says that they are Illumina 1.9 encoded.

[sugo]

Well, if anyone else comes across this problem... Illumina 1.9 FASTQ is indeed equivalent to Sanger input. So I just ran groomer with both the input and output file type set to Sanger. It worked fine after that, though it seems like an unnecessary step. I'm not sure why galaxy doesn't just recognize that the files are already in the right format.

[GenoMax]

Well, if anyone else comes across this problem... Illumina 1.9 FASTQ is indeed equivalent to Sanger input. So I just ran groomer with both the input and output file type set to Sanger. It worked fine after that, though it seems like an unnecessary step. I'm not sure why galaxy doesn't just recognize that the files are already in the right format.

When you know that the data is in "Sanger" format (or any other galaxy supported format) you can edit the metadata (use the pencil button next to the dataset name). You should be able to then set the datatype to "fastqsanger".

[sugo]

Ah, that sounds much easier. Thanks!