Error with annovar
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12 months 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?

annovar • 397 views
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A few points to note:

1. Your question is about annovar, but the only tag added was software error, which is vague and almost irrelevant. Please use relevant tags.
2. Please do not use bold so ubiquitously - it takes away from any effect you might want bolded text to have, and borders on rude.
3. Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (text becomes text), 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.
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Any answers or am I the only one facing this issue.

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Please do not add answers unless you're answering the question. This should have been a comment and I am moving it to one.