2.2.3 - Mapping
In this tutorial we will use Bowtie2. To start, go to the Step-by-Step menu path, Mapping & Counting → Mapping → Bowtie2 and proceed as indicated in Video 9.
Video 9. Mapping step using Bowtie2
Expected results from Mapping analysis
When Bowtie2 is complete, you will receive a bam file per sample with the reads mapped against the reference transcriptome data set.
The expected results of this step are available in the following link Mapping
Remember you can check how the job was completed by accessing the job tracking panel. Pay particular focus on the log file metrics showing the % or reads successfully mapped. An acceptable value is more than 80% of reads mapped per fastq library. If the % is lower than 70% try to preprocess the samples again for better cleaning of the fastq libraries.
To learn more about Bowtie2, see http://bowtie-bio.sourceforge.net/bowtie2/index.shtml