Open TeethBL opened 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.
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