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How to ask FastaAlternateReferenceMaker to keep only the gene without annotation?

Hi,
Basically I am struggling right now as I get fasta files with this type:

Solyc00g005000.2.1 genomic_reference:SL2.40ch00 gene_region:16437-18189 transcript_region:SL2.40ch00:16437..18189+ go_terms:GO:0006508 functional_description:"Aspartic proteinase nepenthesin I (AHRD

V1 **-- A9ZMF9_NEPAL); contains Interpro domain(s) IPR001461 Peptidase A1 "
ATG...CTAG
When I would like to get this one:

Solyc00g005000.2.1

ATG...CTAG
To generate my VCF files I used haplotype caller, and then selected my SNPs with vcftools.

Any idea why this is it? I had done it before and never happen to face that problem...

Please if you have any thoughts.Best,S.

Best Answer

Answers

  • StooffStooff Member

    the '>' did produce a coding inside the question message. but it was :

    '>'Solyc00g005000.2.1 genomic_reference:SL2.40ch00 gene_region:16437-181
    ATG...WHATEVER

    and

    '>'Solyc00g005000.2.1
    ATG...WHATEVER

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