Question: FASTQC for RNA-Seq data in Galaxy
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gravatar for sanathoi.guru
5 months ago by
sanathoi.guru10 wrote:

Hello, I have 3 paired end fastaq file and when i loaded to Galaxy through EBI-SRA, it shows XXX.fastaq.gz, xxx 1.fastaq.gz and xxx 2.fastaq.gz. I was wondering what does the first file mean for (without number)??? 1. when i do FASTQC for this reads, the report shows some low quality. After TRIM sequence or Clip adapters, it can't pass FASTQC test. whats should be the reason? 2.Is FASTQC necessary for RNA-Seq data??

ADD COMMENTlink modified 5 months ago by Devon Ryan1.5k • written 5 months ago by sanathoi.guru10
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gravatar for Devon Ryan
5 months ago by
Devon Ryan1.5k
Germany
Devon Ryan1.5k wrote:

The xxx_1.fastq.gz and xxx_2.fastq.gz files are (likely already trimmed) paired-end files. The xxx.fastq.gz file is likely the file of "orphans" or "singletons" that resulted from the trimming process discarding one of the reads in a pair. In this dataset, it appears that the submitter didn't upload the raw files, but rather what was produced after trimming.

Whether reads will pass all of the FastQC tests will depend largely on the type of dataset. For example, RNAseq datasets will ALWAYS fail some tests. In fact, the only types of datasets that should routinely pass all of the FastQC checks are whole-genome sequencing. If you're worried about a particular test then post the test result and the EBI/SRA accession number so we can see what type of experiment the data is from.

ADD COMMENTlink written 5 months ago by Devon Ryan1.5k

so, if the data is used in RNA-Seq Analysis, Quality check or trimming is not required.. right??

ADD REPLYlink written 5 months ago by sanathoi.guru10

It's always good to have a look at FastQC, just don't expect every test to show "pass". If this is indeed already trimmed then at the very least you shouldn't have to remove adapters.

ADD REPLYlink written 5 months ago by Devon Ryan1.5k
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