Error reading gff file into R (with read.gff from the ape package)
Dear all,
I was trying to read a gff3 genome file into R, but I get the following error:
Error in scan(file, w, sep = "\t", quote = "", quiet = TRUE, na.strings = na.strings, :
scan() expected 'an integer', got 'TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC'
Has anyone seen this and/or knows how to solve it?
Thanks,
Ramiro
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WouterDeCoster
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ramiroricardo •
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ramiroricardo •
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May be you can try
import.gfffunction fromrtracklayer.Few parsers handle GFF files with sequence information. The simplest solution is to just delete the sequence information off of the end.
I encountered the same problem. It is because there are fasta files at the end. Try
grep -n ">" gff_fileto find the fasta files, and then just take the lines before that into a new file which won't give this error.