I have a list of ORF (1159) that i want to extract from a complete metagenomic ORF file that contain 597500 ORF. Is there any tool or script with which i can do that. Or should i do this with assembled contigs, if yes then how can i extract those contgs/ORFs. I want to do blast with only 1159 ORF not with whole metagenomic ORFs. Thank you
Question: Extracting specific ORFs from a complete metagenomic ORF file?
7 months ago by
microbez.uaf • 0
microbez.uaf • 0 wrote:
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6 months ago by
colindaven • 1.7k
Hannover Medical School
colindaven • 1.7k wrote:
What's a metagenomics ORF file ?
If it is a FASTA, you can use
# index the fasta samtools faidx test.fasta #extract orf78 samtools faidx test.fasta orf78 samtools faidx test.fasta orf78 > myORF.fasta
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