http://stab.st-andrews.ac.uk/wiki/index.php?action=history&feed=atom&title=I2rda_m2rx 2026-04-30T11:11:44Z Revision history for this page on the wiki MediaWiki 1.30.0 http://stab.st-andrews.ac.uk/wiki/index.php?title=I2rda_m2rx&diff=1428&oldid=prev 2017-05-04T12:52:56Z

<p>Rf moved page <a href="/wiki/index.php?title=Mapping_to_Reference" title="Mapping to Reference">Mapping to Reference</a> to <a href="/wiki/index.php?title=I2rda_m2rx" title="I2rda m2rx">I2rda m2rx</a></p> <table class="diff diff-contentalign-left" data-mw="interface"> <tr style="vertical-align: top;" lang="en"> <td colspan="1" style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan="1" style="background-color: white; color:black; text-align: center;">Revision as of 12:52, 4 May 2017</td> </tr><tr><td colspan="2" style="text-align: center;" lang="en"><div class="mw-diff-empty">(No difference)</div> </td></tr></table>

Rf http://stab.st-andrews.ac.uk/wiki/index.php?title=I2rda_m2rx&diff=1352&oldid=prev 2017-04-08T23:23:07Z

<p>s1</p> <p><b>New page</b></p><div>= Aims =<br /> <br /> Mapping to a reference genome is a vital step to generate counts and do differential gene expression thereafter. For RNA-Seq data it is important to choose an aligner which is splice aware.<br /> <br /> In this part you will learn to:<br /> * align RNA-Seq reads to a reference genome<br /> * calculate the mapping rate<br /> <br /> You will use the following software:<br /> * TopHat2 v2.0.11: http://ccb.jhu.edu/software/tophat/index.shtml<br /> * Bowtie2 v2.2.0: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml<br /> <br /> The data set you&#039;ll be using is downloaded from ENA (http://www.ebi.ac.uk/ena/data/view/SRP019027). The reads belong to sample SRR769316. The data set is tailored with respect to the time allocated for the exercise.<br /> <br /> Change directory:<br /> <br /> cd /home/training/Data/04_Mapping_to_a_reference_genome<br /> <br /> Index the reference genome using Bowtie2:<br /> <br /> cd Reference<br /> bowtie2-build mm10_chr19-1-20000000.fasta mm10_chr19-1-20000000<br /> <br /> Run the alignment using TopHat2:<br /> <br /> cd ..<br /> tophat2 -o tophat2 --no-mixed \<br /> --rg-id Lane-1 --rg-sample sample1 --rg-center XYZ --rg-platform Illumina \<br /> -G Reference/mm10_chr19-1-20000000_Ensembl.gtf Reference/mm10_chr19-1-20000000 \<br /> /home/training/Data/03_Quality_control_and_data_preprocessing/Read_1.fastq \<br /> /home/training/Data/03_Quality_control_and_data_preprocessing/Read_2.fastq<br /> <br /> where:<br /> * --no-mixed: For paired reads, only report read alignments if both reads in a pair can be mapped<br /> * --rg-id: Read group ID<br /> * --rg-sample: Sample ID<br /> * --rg-center: Sequencing Centre name<br /> * --rg-platform: Sequencing platform descriptor<br /> * -G: Supply TopHat with a set of gene model annotations and/or known transcripts, as a GTF 2.2 or GFF3 formatted file.<br /> * -o: Output directory<br /> <br /> Check the output of TopHat2:<br /> <br /> cd tophat2<br /> ls<br /> <br /> Get the mapping rate:<br /> <br /> cat align_summary.txt<br /> <br /> Get the number of reads mapped.<br /> Run the alignment of filtered data using TopHat2<br /> <br /> cd ..<br /> tophat2 -o tophat2_with_filtered_data --no-mixed \<br /> --rg-id Lane-1 --rg-sample sample1 --rg-center XYZ --rg-platform Illumina \<br /> -G Reference/mm10_chr19-1-20000000_Ensembl.gtf Reference/mm10_chr19-1-20000000 \<br /> /home/training/Data/03_Quality_control_and_data_preprocessing/Read_1_q30l50.fastq \<br /> /home/training/Data/03_Quality_control_and_data_preprocessing/Read_2_q30l50.fastq<br /> <br /> Check the output of TopHat2:<br /> <br /> cd tophat2_with_filtered_data<br /> ls<br /> <br /> Get the mapping rate:<br /> <br /> cat align_summary.txt<br /> <br /> Get the number of reads mapped.<br /> * What difference does using the filtered data make?</div>

Rf