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3.7 years ago
ga23981
•
0
I used the following annovar command to generate refGeneMrna.fa file
usr/local/apps/eb/annovar/2017Jul16-foss-2016b-Perl-5.24.1/retrieve_seq_from_fasta.pl --format refGene --seqfile Pvulgaris_442_v2.0.softmasked.fa Pvulgaris_442_v2.1_refGene.txt --out Pvulgaris_442_v2.1_refGeneMrna.fa
It throws an error:
NOTICE: Reading region file Pvulgaris_442_v2.1_refGene.txt ... Error: invalid record found in 'refGene' file Pvulgaris_442_v2.1_refGene.txt (15 or 16 fields expected): <Phvul.001G000400.1.v2.1 Chr01 - 705 6715 951 6655 6705,3314,3855,4306,6259,6520, 1266,3407,3988,4453,6426,6715,>
I generated the refGene.txt file without any error using the following command:
gtfToGenePred Pvulgaris_442_v2.1.gene.gtf Pvulgaris_442_v2.1_refGene.txt
I got my my gtf file by converting the gff3 to gtf format:
gffread -E Pvulgaris_442_v2.1.gene.gff3 -T -o Pvulgaris_442_v2.1.gene.gtf
How can I get my refGene file in correct format?
A few points to note:
software error
, which is vague and almost irrelevant. Please use relevant tags.code
option) to present your post better. You can use backticks for inline code (`text` becomestext
), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.Any answers or am I the only one facing this issue.
Please do not add answers unless you're answering the question. This should have been a comment and I am moving it to one.