batch retrieval/copy the fasta sequences from the assembly file
I have around 30,000 transcripts fasta with different contig (sequence) names. I want to pick (batch retrieval or copy) specific contigs like MK200500, MK300200, MK241000....Doing it manually would be too much time and energy spending. Is there any automatic way to batch retrieval/copy the fasta sequences given the names?
1 answer
This is one of FAQ on Biostars. I will link one thread that has answers: Extract fasta sequences from a file using a list in another file. There are others (Retrieve a subset of FASTA from large Illumina multi-FASTA file ). This Q will likely be closed as a duplicate.
Log in to answer this question.
More posts like this
-
Finding ORFs in a FASTA file
written by Melissa •
-
Extracting CDS from fragmented assemblies
written by ebaldwin •
-
How to extract variable nucleotide regions from a list of contigs
written by kayrouz.1 •
-
Add contig lenght to VCF header in a robust way
written by William
-
Limit the number of results in NCBI search result
written by The Last Word
-
Obtaining contig stats from Velvet+Oases De Novo Assembly
written by blazer9131 •
-
Mitochondrial denovo assembly
written by mandar.bobade •
-
Is There Such A Way/ Program To Do This...
written by Biogeek
-
Id In Oases Pipeline Stats.Txt File
written by Charles Warden
-
How To Retrieve Fasta Sequences By Gene Symbols In Multiple Query?
written by giorgiocasaburi85 •
