The next step I need to do is pulling out the mitogenomes, I heard of two options, grep and using NOVOPLASTY, but I cant find a tutorial that can explain how to extract this from a fasta format I'd appreciate your help, thank you
- write HELP in capitals in your title - it isn't good manners and won't help you get an answer.
- post large screenshots of text (such as commands, file names and text file contents). It is better to copy and paste those as text inside your question, preferably using the formatting buttons to structure your post.
- explain in detail your problem. For example, what is the "own database" you created? Why do you have several "own databases"? Do you have one contig per file, and many fasta files, or each fasta contains multiple contigs? What is the contents of the
namelistfiles? Do you intend to pull the contigs from the database or from the fastas with contigs?
Some general comments on your code:
1) don't use
for i in `ls ANT198n.fasta*`
It is error-prone, use instead:
for i in ANT198n.fasta*
2) As far as I can tell from your screenshots,
ls ANT198n.fasta* will return
ANT198n.fasta, so you are using a
for loop to loop over just one file - that is, the for loop is unnecessary.
Finally, assuming you want to pull out the hits from the fasta files, you can use samtools:
samtools faidx ANT198n.fasta samtools faidx ANT198n.fasta $(cat ANT198n.fasta,namelist) > csulcatus.mt.fasta