Day3.2: A look at our alignments

Submit a job to CAMERA

You’ll find in your home folder a new directory called “files“. Inside it we put a random selection of reads from both RNA-Seq and WGS (called like rrna.geno-XX.fasta and gdna.geno-XX.fasta).
Submit both to CAMERA using a proper analysis.

A look at our outputs

We launched a BLAST alignment of short reads against a 16S ribosomal database (using -m 8 for tabular output), and we did the same using PASS (asking for SAM output).

You will find both outputs in the “files” directory, in your home. Today we’ll play with pass_output.sam from PASS.

Open a Terminal and go to the “files” directory. Start inspecting the PASS output with:

less -S pass_output.sam

Remember that less is an interactive viewer, you can scroll pages and exit typing “q”. Open the SAM file specifications to recall the meaning of this field.

Classify Ribosomal sequences

Now we are going to try a sequence classification using a program written by Nicola Vitulo in our group. This program uses the “Lowest Common Ancestor” method to assign each read to a node in the taxonomical tree.
To do so, it analyze the output of an alignment (SAM format) against a 16S rRNA database.

riboclass [file_sam] > [output.txt]

Change file_sam with the PASS output and save the riboclass output in the “dir-01” directory, calling it “riboclass.txt“. Wait for the program to finish and look at the results.

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