How to fetch gene bank flat file (.gb) in R
Hello, I need to fetch gene bank flat file of bacteria (Mycobacterium_smegmatis) in R. I have tried using Biofiles. It's not working and generating the error as below
Error in biofiles::gbRecord(mito.path) :
'rcd' must be the path to GenBank or Embl flat file or an 'efetch' object containing GenBank records
Please suggest me how can I do that.
Thank you
• 1,591 views
•
link
updated
by
WouterDeCoster
•
written
by
Neu •
•
written
by
Neu •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Getting cds files from ncbi using accession numbers
written by lily •
-
ncbi error report log for validate fastq issue
written by 1769mkc
-
Help with error makeTxDbFromGFF in GenomicFeatures package
written by Chris •
-
Non-standard Genbank format
written by mrmrwinter •
-
ValueError: Need a Nucleotide or Protein alphabet. Trying to write a Genbank file and getting error
written by Fishy_DNA •
-
Copy number variation study using CNOGpro
written by Neu •
-
Mal-formed sequence line error in Bio.SeqIO
written by stueckmann.daniel •
-
DeSeq2 error correction and experiment design
written by abseq •
-
Entrez Direct problems
written by ioanahrom •
-
Fetching Genbank records and parsing them to be DNAStringset objects
written by peter.durr •
Please provide the code that gives this error.
What the error message says is that mito.path is not a valid path to a Genbank file nor an efetch object. If you're trying to read a file, make sure that it's accessible to your script.