Question: Extracting specific ORFs from a complete metagenomic ORF file?
0
gravatar for microbez.uaf
5 weeks ago by
microbez.uaf0 wrote:

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

sequencing assembly gene • 122 views
ADD COMMENTlink modified 4 weeks ago by colindaven1.2k • written 5 weeks ago by microbez.uaf0
3
gravatar for colindaven
4 weeks ago by
colindaven1.2k
Hannover Medical School
colindaven1.2k 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
ADD COMMENTlink written 4 weeks ago by colindaven1.2k

Hye Collin, Thanks for your response. I have contigs and translated ORFs from those contigs (Approximately 900,000 contigs and 597500 translated ORFs) . I want to extract specific contigs/ORFs (1159) from those files. Can you help me in this regard.

ADD REPLYlink written 26 days ago by microbez.uaf0
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