Difference between revisions of "Team:Uppsala/Transcriptomics/Bioinformatics"
| Line 320: | Line 320: | ||
| − | + | <h1>Bioinformatics</h1> | |
| Line 327: | Line 327: | ||
Most of the tools we used were available through the free website Usegalaxy.org which as well let us do the processing on their servers. Because we also made use of nanopore sequencing, tailored tools used for the MinION data were available from their community hub which could be run from a terminal window. </p><br><br> | Most of the tools we used were available through the free website Usegalaxy.org which as well let us do the processing on their servers. Because we also made use of nanopore sequencing, tailored tools used for the MinION data were available from their community hub which could be run from a terminal window. </p><br><br> | ||
| − | < | + | <h2>Experiment</h2> |
<p>We decided to create our bioinformatics pipeline from scratch. Generally, a basic transcriptomics pipeline looks like the following: Alignment to a reference genome, gene counting and differential gene expression. However a couple of data processing steps were needed for the nanopore data beforehand such as demultiplexing and adapter trimming.</p><br><br> | <p>We decided to create our bioinformatics pipeline from scratch. Generally, a basic transcriptomics pipeline looks like the following: Alignment to a reference genome, gene counting and differential gene expression. However a couple of data processing steps were needed for the nanopore data beforehand such as demultiplexing and adapter trimming.</p><br><br> | ||
| − | < | + | <h3>Demultiplexing and adapter trimming</h3> |
| + | <p>Because the sequencing itself runs pooled samples containing both the barcoded cultured- and control-group samples, the data produced needs to be demultiplexed i.e separated into files containing the reads from respective groups. Because the barcodes used to fingerprint each group is made up of its own base sequence, this also had to be removed or ”trimmed” from the data, leaving us with the pure mRNA sequences. This was achieved using a free nanopore community tool called porechop.</p> | ||
Revision as of 17:00, 15 October 2018
:root{ --primary: #8b1a32; --secondary:#969696; --tertiary: #f15025; --whiteish: #fcf7ff; --light-blue:#cde6f5; --alt-secondary: #554640; } html{ width: 100%; height: 100%; } *{ margin: 0; padding: 0; box-sizing: border-box; } .parallax { /* The image used */ background-image: url("https://static.igem.org/mediawiki/2018/9/99/T--Uppsala--Transcriptomics-HEADER_2.jpeg"); /* Set a specific height */ min-height: 99vh; /* Create the parallax scrolling effect */ background-attachment: fixed; background-position: center; background-repeat: no-repeat; background-size: cover; /*background: linear-gradient(to bottom, transparent 90%);*/ } .blur-box { background-color: var(--whiteish); box-shadow: 0 0 10px 10px var(--whiteish); } .sub-header{ /* Set a specific height */ height:20vw; min-height: 150px; /* Create the parallax scrolling effect */ /*background-attachment: fixed;*/ background-position: center; background-repeat: no-repeat; background-size: cover; } .sub-header h1{ font-size: 60; text-align: center; position:absolute; left:0; right:0; margin-top:6.5% ; margin-left:auto; margin-right: auto; color:white; bottom: px; } /* TODO: CHANGE */ #blue{ background-image: url(redbanner.jpg); } h1, h2{ color: #661325; } h1{ margin-top:2em; margin-bottom: 0.5em; } #first-title{ top:100px; margin-top: 0; } .content{ position:relative; background-color: var(--whiteish); } .content-text{ margin-top:2em; min-width: 400px; width:70%; position: relative; margin: auto; /*background-color: #8c7cff;*/ } .scroll-pointer{ top:85%; position:absolute; /*margin-left:auto; margin-right:auto;*/ width: 100%; padding: 0; } .scroll-pointer img{ color: var(--primary) ; } .center-icon{ width:100px; position: relative; display: block; margin-right: auto; margin-left: auto; opacity: 0.8; } .center { display: block; margin-left: auto; margin-right: auto; width: 50%; }
Bioinformatics
After a succesfull sequencing has been performed and you’re left with raw data containing millions and millions (and millions) of lines of base sequences, all of this needs to be processed and interpreted. This is where the interdisciplinary field of bioinformatics comes in. A vast range of software tools are available, tailored to different kinds of analysis as well as being unique to the different sequencing methods being used.
Most of the tools we used were available through the free website Usegalaxy.org which as well let us do the processing on their servers. Because we also made use of nanopore sequencing, tailored tools used for the MinION data were available from their community hub which could be run from a terminal window.
Experiment
We decided to create our bioinformatics pipeline from scratch. Generally, a basic transcriptomics pipeline looks like the following: Alignment to a reference genome, gene counting and differential gene expression. However a couple of data processing steps were needed for the nanopore data beforehand such as demultiplexing and adapter trimming.
Demultiplexing and adapter trimming
Because the sequencing itself runs pooled samples containing both the barcoded cultured- and control-group samples, the data produced needs to be demultiplexed i.e separated into files containing the reads from respective groups. Because the barcodes used to fingerprint each group is made up of its own base sequence, this also had to be removed or ”trimmed” from the data, leaving us with the pure mRNA sequences. This was achieved using a free nanopore community tool called porechop.