gcremers
commented
1 year ago Hi Saras,
When you go to the main directory of your results, you'll find two files (total.ovw and total.tsv), which contain an overview of all the key genes of all samples. There is also a metagenome.tsv file, which contains the names of all the genes found in the analysis. You can use grep to search for the genes you want.
If you want the fasta files you can use the fastaextract scripts to get those using (from within the main directory of your results): for dir in */; do cd $dir && /path/to/fastaextract_desc_id.pl *.all.faa methanol ../methanol && cd ..; done
where the first methanol is a search term you can use to search through the headers of each fastasequence. The second methanol is the base for the name of the newly formed file. In this case it would be methanol.fasta The other fasta script can be used in similar to search through the sequences themselves.
If you notice there is also a ovw and tsv file in the directory for the MAG. These are the (key)genes for the single MAG.
Creating a heatmap isn't something Metascan can do, so I'm afraid I can't help you with that one.
Hi! @gcremers Thanks for help earlier, I successfully ran metacsan for a single MAG. Now I want to run metascan for muptiple MAGs and also I wanted to ask that is it possible to create a merged output file for all the MAGs and then extract genes responsible for nitrogen metabolism and make a heatmap.
Thanks in Advance! Saras :)