DENOVOSEQ - PREPROCESSING YOUR RAW READS


Preprocessing is required to prepare fastq libraries for mapping the next step of the protocol. The drop-down submenu for preprocessing organizes the interfaces to call the preprocessing tools according to their utility and functions: quality analysis, demultiplex, trimming clipping and/filtering of raw reads to eliminate primer/adapter remnants, artifacts or low quality sequences and/or other preprocessing (Prepseq) actions. Following is a brief detail about how to manage them in the step-to-step workflow.

Figure 5: Drop down menu for preprocessing.

2.1 - QUALITY ANALYSIS

- Quality Analysis: FastQC

FastQC (Andrews 2016) aprovides a simple way to do quality control checks on raw sequence data. It provides a modular set of analyses, you can use to obtain a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. See the FastQC manual at https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ for more information.

To run FASTQC with DeNovoSeq go to:

            [ Preprocessing → Quality Analysis → FastQC ]

Figure 6: Animated GIF of using a FASTQC application.

You will get a confirmation message that the job has been launched. Otherwise, check all options again. If an input field is invalid or missing you will get an error icon beside the field (hover the mouse over it to see the error message).

2.2 - DEMULTIPLEX

- Demultiplex: FastqMidCleaner

FastqMidCleaner splits sequencing reads of a fastq file according to a set of given MIDs.

To run FastqMidCleaner with DeNovoSeq go to:

            [ Preprocessing → Demultiplex → FastqMidCleaner ]

Figure 7: Animated GIF of using a FASTQMidCleaner application.

You will get a confirmation message that the job has been launched. Otherwise check all options again.

2.3 - TRIMMING AND CLEANING

- Trimming & Cleaning: Cutadapt

Cutadapt (Martin 2011) finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequences from your sequencing reads. See the Cutadapt manual at https://cutadapt.readthedocs.io/en/stable/guide.html for more information.

To run Cutadapt with DeNovoSeq go to:

            [ Preprocessing → Trimming & Cleaning → Cutadapt ]

Figure 8: Animated GIF of using a Cutadapt application.

You will get a confirmation message that the job has been launched. Otherwise check all options again.

- Trimming & Cleaning: Prinseq

PRINSEQ (Schmieder and Edwards 2011) can be used to filter, reformat, or trim your sequencing reads. See the Prinseq manual at http://prinseq.sourceforge.net for more information.

To run Prinseq with DeNovoSeq go to:

            [ Preprocessing → Trimming & Cleaning → Prinseq ]

Figure 9: Animated GIF of using a PrinSeq application.

You will get a confirmation message that the job has been launched. Otherwise check all options again.

- Trimming & Cleaning: Fastx-ToolKit

The FASTX-Toolkit (Hannon Lab 2016) iis a collection of tools for preprocessing of Fasta/Fastq files. See “the Fastx-Toolkit manual at here for more information.

To run any of the Fastx-ToolKit tools with DeNovoSeq go to

           [ Preprocessing → Trimming & Cleaning → Fastx-Toolkit ]

Then select the desired tool from the sub-menu.

            The sub-menu includes:


Figure 10: Animated GIF of using a FastX Toolkit application.

You will get a confirmation message that the job has been launched. Otherwise check all options again.

2.4 - PREPSEQ

- PrepSeq:FastqCollapser

FastqCollapser removes duplicate reads from fastq files (Based on sequence content).

To run FastqCollapser with DeNovoSeq go to:

            [ Preprocessing → PrepSeq → FastqCollapser ]

Figure 11: Animated GIF of using a FastQCollapser application.

You will get a confirmation message that the job has been launched. Otherwise check all options again.

- Trimming & Cleaning: FastqIntersect

FastqIntersect gets two fastq paired end files that have been independently preprocessed and performs an intersection between the reads of both files to keep only the mate reads that are present in both files. If both files does not have the same sequence order, it automatically sorts output file #2’s following file #1’s order.

To run FastqIntersect with DeNovoSeq go to:

            [ Preprocessing → PrepSeq → FastqIntersect ]

Figure 12: Animated GIF of using a FastQCollapser application.

You will get a confirmation message that the job has been launched. Otherwise check all options again.







GPRO licensing and Usage           Former versions           TSI-100903-2019-11

Biotechvana


Valencia Lab
Parc Cientific Universitat de Valencia
Carrer del Catedràtic Agustín Escardino, 9. 46980 Paterna (Valencia) Spain
Madrid Lab
Parque Científico de Madrid
Campus de Cantoblanco
Calle Faraday 7, 28049 Madrid Spain
Contact us
Phone: +34 960 06 74 93
Email: biotechvana@biotechvana.com

Supported by


Hipra Scientific S.L.U, Polypeptide Therapeutic Solutions S.L., Biotechvana S.L. and Nostrum Biodiscovery constitute the consortium of enterprises participating in the project "Research of a new vaccine for a human respiratory disease", granted by the CDTI (Center for Industrial Technological Development), and supported by the Ministry of Science and Innovation and financed by the European Union – NextGenerationEU. The main objective of this project is to design a safe immunogenic and effective vaccine against the respiratory syncytial virus.

Biotechvana © 2015
Privacy policy
Política de privacidad
This website use cookies, by continuing to browse the site you are agreeing to our use of cookies. More info about our cookies here.