Question: Trimmomatic works good?
0
gravatar for caalvarador
2.3 years ago by
caalvarador0 wrote:

Hi, I am newbie in data analysis of RNAseq. I have tried to remove the illumna adapters by trimmomatic tool, but I have not been able choose the Input FASTQ file, the button of options don't display my files. Please help me. Do I need to do something anymore before?. Obviously I uploaded the FASTQ files to Galaxy. Will be a problem of Galaxy platform? Thanks.

rna-seq • 1.4k views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by caalvarador0
2
gravatar for vladimir.gritsenko
2.3 years ago by
Tel Aviv University
vladimir.gritsenko90 wrote:

There are a number of versions of the FASTQ format. Galaxy tools like working with 'fastqsanger', but by default your FASTQ is marked as just 'fastq'. You can view and edit this by clicking the pen icon next to your dataset ('Edit attributes') and then going to the datatype tab. But don't change type unless you absolutely know what it is!

To discover the actual type of your FASTQ, you can run FASTQC on it. Under the basic statistics there will be an 'Encoding' field. If it is 'Sanger / Illumina 1.8' (or above 1.8), I think that you can change the datatype to 'fastqsanger' directly. If not, or if you're not sure (or if I was wrong and this isn't working for you), run the FASTQ groomer tool on your original FASTQ files, and that will yield the correct format which the other tools can work with.

ADD COMMENTlink written 2.3 years ago by vladimir.gritsenko90
0
gravatar for caalvarador
2.3 years ago by
caalvarador0 wrote:

Hi, I've used groomer for the sequences and it worked!!, the encoding is Sanger / Illumina 1.9. Thank you very much.

ADD COMMENTlink written 2.3 years ago by caalvarador0
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