search

MadsAlbertsen / mmgenome

Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes
https://kasperskytte.github.io/mmgenome2/
27 stars 8 forks source link

How to generate "tax.txt" #34

Open TeethBL opened 7 years ago

TeethBL commented 7 years ago

Hi Everyone,

I am a beginner on metagenome binning. Following the instructions, I am preparing my own R data sets.

In the file "rRNA.sh", the "16S.fa" could be generated, however the generation of "tax.txt" was not mentioned:

"makeblastdb -in assembly.fa -dbtype nucl > temp.blast2 blastn -query /space/users/malber06/Desktop/Databases/gg_90id/gg_90.fasta -db assembly.fa -num_threads 60 -max_target_seqs 5 -outfmt 6 -evalue 1e-10 -out temp.blast.txt

perl /space/users/malber06/mmgenome/scripts/extract.long.hits.from.blast.pl -b temp.blast.txt -d assembly.fa -m 500 -o 16S.fa"

Could anyone clue me in Regards

Chen

vrbrand commented 7 years ago

"tax.txt" should be generated with the Data Generation Shell Script available in the Workflows folder. Running through the script, it predicts proteins with Prodigal, runs an HMM search to find essential genes with HMMER (and creates "essential.txt"), blasts the essential genes, and finally, extracts the consensus taxonomic assignment with MEGAN. This last step generates the "tax.txt" file.