2. Read based analysis

Session 2: 14:00-15:30

Table of contents

1. Gene Prediction
2. Identification of rDNA in metagenomic samples
3. Gene annotation

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Gene prediction

One of the main tasks in metagenomics is to find which potential functions are present in our samples. There are different approaches to achieve this goal, for example the most straightforward one we can do, is to perform a translated similarity search (blastx) against a protein database using the reads. However, this approach has some caveats: for example, our results will be biased to the content of the database; doing this search using all reads against a large database like the NCBI protein non-redundant (nr) is computationally really expensive; or we are losing the higher sensitivity and specificity power of using profile based methods for searching protein domain databases like PFAM. A good approach to avoid all this problems is to do an ab-initio gene prediction with tools designed specifically to deal with fragmented sequences like the ones we will find in short reads or assembled sequences. A good review about different gene prediction tools applied to short-reads and the particularities of this prediction can be found here

For our reads we will use FragGeneScan. FragGeneScan is used by MG-RAST and the EBI MG-Portal. Analysing OSD102 will take roughly 32 minutes using only one core in our BioLinux virtual machine. You already will find the pre-computed results of this sample in your folder. Nevertheless, we will learn using FragGeneScan with a smaller file which we will create.

First we need to transform the merged sequences from fastq to fasta to be able to be process the sequences using FragGeneScan. This is an easy task with one of the scripts present in BBtools:

cd ~/Desktop/microbeco_course/analysis/0-pre-processing/2-quality-trimming/merged

reformat.sh in=OSD102.qc.fastq out=OSD102.qc.fasta

Next, we will extract 1000 reads and we will do the gene prediction:

cd ~/Desktop/microbeco_course/analysis/1-read-level-analysis/0-gene-prediction

mkdir FGS-test

cd FGS-test

reformat.sh in=~/Desktop/microbeco_course/analysis/0-pre-processing/2-quality-trimming/merged/OSD102.qc.fasta out=OSD102.qc.1000.fasta reads=1000

Now we can run FragGeneScan on these 1000 merged reads in fasta format:

run_FragGeneScan.pl -genome OSD102.qc.1000.fasta -out OSD102.1000 -complete 0 -train illumina_5

In case we would like to run the gene prediction on the whole dataset we should do:

run_FragGeneScan.pl -genome ~/Desktop/microbeco_course/analysis/0-pre-processing/2-quality-trimming/merged/OSD102.qc.fasta -out OSD102 -complete 0 -train illumina_5

We can easily get some statistics on the predicted sequences using one tiny utility from Sean Eddy in SQUID

cd ~/Desktop/microbeco_course/analysis/1-read-level-analysis/0-gene-prediction

seqstat OSD102.faa

seqstat OSD102.ffn

We can count sequences easily using grep :

grep -c '>' OSD102.faa

How many genes does FGS predict? What is the mean length of the nucleotide sequences? and of the amino acid sequences?

Identification of rDNA in metagenomic samples

In shotgun metagenomic sequences we can also identify rDNA fragments and perform a taxonomic classification in a similar fashion we do with amplicon data. There are different approaches to identify rDNAs in metagenomic samples, we can use profile methods approaches like rRNASelector, filtering algorithms like SortMeRNA,sequence similarity searches using blastn or more complex using more complex sequence aligners like PyNAST or SINA. All this methods rely on some of the specialised rRNA databases like RDP, GreenGenes or SILVA. We will use SortMeRNA, it has a trade-off between accuracy and speed using SILVA as reference database. Afterwards, we will perform the taxonomic annotation using SILVAngs.

To use SortMeRNA first we need to index the databases:

cd ~/Desktop/microbeco_course/analysis/1-read-level-analysis/1-rRNA-identification

indexdb_rna --ref /usr/local/bioinf/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta,/usr/local/bioinf/sortmerna/index/silva-bac-16s-db:\
/usr/local/bioinf/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta,/usr/local/bioinf/sortmerna/index/silva-arc-16s-db:\
/usr/local/bioinf/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta,/usr/local/bioinf/sortmerna/index/silva-euk-18s-db

And then we will be ready to identify the reads which are potentially rDNAs:

sortmerna --reads ~/Desktop/microbeco_course/analysis/0-pre-processing/2-quality-trimming/merged/OSD102.qc.fasta\
    --ref /usr/local/bioinf/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta,/usr/local/bioinf/sortmerna/index/silva-bac-16s-db:\
	     /usr/local/bioinf/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta,/usr/local/bioinf/sortmerna/index/silva-arc-16s-db:\
	     /usr/local/bioinf/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta,/usr/local/bioinf/sortmerna/index/silva-euk-18s-db \
    --fastx \
    --aligned OSD102_rDNA

Before submitting the sequences to SILVAngs we should check if we have duplicated headers. SILVAngs only uses the first field of the fasta header. If we have a look at our sequences, we see that we have duplicates:

cd /home/manager/Desktop/microbeco_course/analysis/1-read-level-analysis/1-rRNA-identification

grep '>' OSD102_rRNA.fasta | cut -f1 -d ' '| sort | uniq -d | head -n 10

We can use some awk magic to remove the space on the fasta header:

awk '{$0 ~ /^>/ ? gsub(" ","_") : $0; print}' OSD102_rDNA.fasta OSD102_rDNA.silvangs.fasta

or we can follow a much easier approach using reformat.sh from BBtools:

reformat.sh in=OSD102_rDNA.fasta out=OSD102_rDNA.silvangs.fasta underscore=t

Now we will be ready to upload the file OSD102_rDNA.silvangs.fasta to SILVAngs. The sequences have been already analysed and you can get the results from:

wget 'https://owncloud.mpi-bremen.de/index.php/s/eaB3ChiDG6i9C6M/download?path=%2Fcourses%2Fmetagenomics%2Fmicrobeco2015%2FSILVAngs&files=resultarchive-Microbeco_course_2015.zip' -O Microbeco2015-SILVAngs.zip

We will have a look at the Krona plots to see the different taxonomic classifications:

unzip Microbeco2015-SILVAngs.zip

firefox results/ssu/tax_breakdown/krona/microbeco_course_2015---ssu---krona----Total---sim_93---tax_silva---td_20.html &

Gene annotation

Now, that we identified the potential genes in our metagenomic samples, we can start to look for the functions they encode. Depending on the questions we have, we can use a more targeted approach. For example focusing on one single gene or taxonomic group, or we can do the annotation of the whole metagenomic sample. Depending on our computational resources, we can do it using our own facilities or we can use any of the public resources like MG-RAST or EBI Metagenomics Portal. Usually these resources use a variety of biological databases, which we can use too - in a local manner - depending on what we want to ask our metagenomic samples. Some of those databases are PFAM, KEGG, eggNOG, COG....

OSD102 has been already analysed at EBI-MG portal. And also in MG-RAST (login details provided during the course)