Mapping short reads
- synopsis
Asela Wijeratne<awijeratne@astate.edu>
rest
If you are using genome as the reference for RNAseq reads, you will need to use a splice-aware aligner like Tophat2. If you are using cDNA as the reference, you can use a general purpose aligner like Bowtie2.
You need to do only one of the procedures based on what your group have been assigned to.
- Click on App.
- In the finder window type "Tophat"
- As indicated in the figure, Name your analysis as you want.
- Select the output folder where your analysis is going to be.
- Click on the Green "+" sign.
8. Navigate to the folder where your samples are located. Select only the first read files. Click "OK". You can select all three of your first read files.
- Scroll down and click on the "+" below "Fastq file(s) (Read 2 of paired end reads):"
- Click on App.
- In the finder window type "Bowtie".
3. Select Bowtie app indicated in the figure.
- As indicated in the figure, Name your analysis as you want.
- Click on "Input"
8. Navigate to the folder where your samples are located. Select first and second read files. You can only input one sample at a time.