FastQC-plus 0.10.1 (multi-file)
- Roger Barthelson
FastQC-plus 0.10.1 (multi-file)
FastQC-plus aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. This version runs the application on multiple files and creates a summary output page for all files in .html format.
Quick Start
- To use FastQC, upload your data in FASTQ format.
- Resources: FastQC Help Pages
NOTE: FastQC will determine the format that your FASTQ reads are in (PHRED33, Illumina, etc). The detected read type will be listed on the graphs outputted. As an additional note, PHRED33 is exactly the same as Solexa / Illumina 1.9, thus if using these FASTQ files in downstream apps such as the FASTX toolkit, you will need to select PHRED33 for your format type if your reads are in Solexa/Illumina 1.9 format.
Test DataCommunity Data > iplantcollaborative > example_data > fastqc_plus > inputs
Input File(s):ATreads.fq and ATreads2.fq
fastq files
Parameters Used in AppNo parameters
Output File(s)fastqc_summary.html contains a summarized report for all entries. Original FastQC outputs placed in the intermediate_files directory.
Community Data > iplantcollaborative > example_data > fastqc_plus > output2