Error with getSeq from opened fasta file (Rsamtools 2.0.2) #12
Description
Hi,
I am using Rsamtools 2.0.2, and I have faced an issue on reading sequences from fasta files.
My issue is similar to #5 , but not exactly. When I try to "getSeq" from fasta file I get an error message. This is my script:
GTFfile = "Homo_sapiens.GRCh37.87.gtf"
FASTAfile = "Homo_sapiens.GRCh37.dna.toplevel.fa"
FASTA <- FaFile(FASTAfile)
open(FASTA)
getSeq(FASTA, GRanges("chr1", IRanges(1,5)))
I get this:
Error in value[3L] : record 1 (chr1:1-5) failed
file: Homo_sapiens.GRCh37.dna.toplevel.fa
If I run it in Windows, I get this:
[E::faidx_fetch_seq2] Failed to retrieve block. (Seeking in a compressed, .gzi unindexed, file?)
Error in value[3L] : record 1 (chr1:1-5) failed
file: Homo_sapiens.GRCh37.dna.toplevel.fa
The reference files are standard ensembl reference files and are downloaded from ftp://ftp.ensembl.org/pub/grch37/release-87/fasta/homo_sapiens/dna .
Thank you for your help.
Farshad