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Updated Practical 6 MAG analyses (markdown) authored by Luis H Orellana (Coto)'s avatar Luis H Orellana (Coto)
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Practical-6-MAG-analyses.md
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...@@ -44,12 +44,12 @@ Q.maxbin.006 k__Bacteria (UID203) 5449 104 58 22 27 55 0 0 0 65.52 27.43 0.00 ...@@ -44,12 +44,12 @@ Q.maxbin.006 k__Bacteria (UID203) 5449 104 58 22 27 55 0 0 0 65.52 27.43 0.00
What do you think about the quality of these bins? In the following activities we will be analyzing some of them using anvi'o. For now, let's analyze them a little further. We can ask checkM to give us a bit more taxonomical information using the `checkm tree` function incorporated in checkM. What do you think about the quality of these bins? In the following activities we will be analyzing some of them using anvi'o. For now, let's analyze them a little further. We can ask checkM to give us a bit more taxonomical information using the `checkm tree` function incorporated in checkM.
``` ```
$ checkm tree_qa 01.selected-Bacteroidetes-comp90/ -o 2 -f detailed_checkM_selected-21 --tab_table $ checkm tree_qa out-checkm-allbins/ -o 2 -f detailed_checkM-allbins --tab_table
``` ```
Based on checkM genome tree the “closest” relatives in the checkM tree for the bin ACF_bins.006 are: Based on checkM genome tree the “closest” relatives in the checkM tree for the bin U.maxbin.012 are:
``` ```
Bin Id # unique markers (of 43) # multi-copy Insertion branch UID Taxonomy (contained) Taxonomy (sister lineage) GC Genome size (Mbp) Gene count Coding density Translation table # descendant genomes Lineage: GC mean Lineage: GC std Lineage: genome size (Mbp) mean Lineage: genome size (Mbp) std Lineage: gene count mean Lineage: gene count std Bin Id # unique markers (of 43) # multi-copy Insertion branch UID Taxonomy (contained) Taxonomy (sister lineage) GC Genome size (Mbp) Gene count Coding density Translation table # descendant genomes Lineage: GC mean Lineage: GC std Lineage: genome size (Mbp) mean Lineage: genome size (Mbp) std Lineage: gene count mean Lineage: gene count std
ACF_bins.006 43 0 UID3410 k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae g__Roseobacter;s__Roseobacter_RCA_cluster 55.0641913186 2.492471 2492 0.9240893876 11 3 46.7395683218 7.40025086417 2.92510366667 0.555401840516 2984.0 614.866381149 U.maxbin.012 41 0 UID3398 k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae g__;s__ 51.6079429195 3.427858 3796 0.883138974835 11 9 58.9159876191 2.34719045897 4.32964955556 0.425642799849 4296.55555556 377.714504505
``` ```
Keep in mind that you could also evaluate the completeness and contamination of MAGs by finding ‘essential’ protein sequences. Take a look at the ‘HMM.essential.rb’ script found in the course folder. This script is part of a larger collection of tools available at https://github.com/lmrodriguezr/enveomics. If you are interested in doing other meta(genomic) analyses, you will find many other useful scripts in this repository. Keep in mind that you could also evaluate the completeness and contamination of MAGs by finding ‘essential’ protein sequences. Take a look at the ‘HMM.essential.rb’ script found in the course folder. This script is part of a larger collection of tools available at https://github.com/lmrodriguezr/enveomics. If you are interested in doing other meta(genomic) analyses, you will find many other useful scripts in this repository.
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