What is FastQC used for?

What is FastQC used for?

FastQC, written by Simon Andrews of Babraham Bioinformatics, is a very popular tool used to provide an overview of basic quality control metrics for raw next generation sequencing data. There are a number different analyses (called modules) that may be performed on a sequence data set.

When should I run FastQC?

Question: When should the FastQC software be used to QC 10x data? Answer: You may wish to run FastQC if you suspect poor sequencing quality or have some ‘N’s in the barcodes. Low valid barcodes also result in a certain loss of reads, thus a low median gene count per cell.

How do I run FastQC?

Actually installing FastQC is as simple as unzipping the zip file it comes in into a suitable location. That’s it. Once unzipped it’s ready to go. You can run FastQC in one of two modes, either as an interactive graphical application in which you can dynamically load FastQ files and view their results.

How much memory is FastQC?

FastQC cannot use multiple processors per input file. So 1 node, 1 task or processor, 10gb for memory and 1 hour for wall time should be enough.

How do I run FastQC in terminal?

Open a terminal (“Ctrl+Alt+t”) and go to the FastQC folder. You will see that your fastqc folder has been added to the default search PATH that Linux is using to find commands/applications/software.

How do I run FastQC on a Mac?

ramongallego commented on Aug 9, 2018

  1. Download and expand FastQC-0.11. tar. gz.
  2. Navigate to the expanded folder.
  3. run chmod +x fastqc`
  4. sudo ln -s /Absolute/path/to/fastqc /usr/local/bin/fastqc.

What should you pay attention to in the FastQC report?

What should you pay attention to in the FastQC report? Which file is of better quality? Pay special attention to the per base sequence quality and sequence length distribution. Explanations for the various quality modules can be found here.

How does de novo assembly work?

De novo sequencing refers to sequencing a novel genome where there is no reference sequence available for alignment. Sequence reads are assembled as contigs, and the coverage quality of de novo sequence data depends on the size and continuity of the contigs (ie, the number of gaps in the data).

How do I check quality of Fastq files?

This functionality can be found under Tools → FASTQ Tools → FASTQ Quality Check. The wizard allows to select input files and adjust analysis parameters (Figure 2).

Is there a manual for fastfastqc?

FastQC has a really well documented manual page with detailed explanations about every plot in the report. Within our report, a summary of all of the modules is given on the left-hand side of the report.

What’s new in FastQC 3-5-12?

3-5-12: Version 0.10.1 released Added a workround to allow the analysis of concatenated gzipped files Fixed a bug when FastQC was installed in a path containing characters needing to be escaped in a URL Added an option to specify the location of the java interpreter on the command line

What’s new in FastQC for Java?

Fixed a bug when FastQC was installed in a path containing characters needing to be escaped in a URL Added an option to specify the location of the java interpreter on the command line 9-9-11: Version 0.10.0 released

How do I open the FastQC report on Rackham?

The output from FastQC is a HTML report that should be opened in a web browser. When you have X-forwarding enabled you can open it on Rackham with this command: It can be slow to look at graphical files via SSH.