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Commit f8cbf714 authored by Helene Rimbert's avatar Helene Rimbert
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BUG : fixed bad rescue on target with gmap

parent 1422ec20
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1 merge request!9BUG : fixed bad rescue on target with gmap
......@@ -53,16 +53,21 @@ do
echo " Gene $geneid has status UNMAPPED: mapping on the whole genome"
cat $rootdir'/query.mrna.fasta' >> $unmappedMrnaFasta && rm $rootdir'/query.mrna.fasta'
#targetindex=$gmapdb
#targetindexdir=$gmapdbdir
#targetgff=$rootdir'/gmap.wholeGenome.gff3'
#gmapexe='gmapl'
#eval $gmapexe --min-identity 0.80 --min-trimmed-coverage 0.50 --ordered -n 1 -d $targetindex -D $targetindexdir -f 2 $rootdir'/query.mrna.fasta' 1> $targetgff 2> $rootdir'/gmap.wg.log' && rm $rootdir'/query.mrna.fasta'
else
echo "running gmap on target"
elif [ -f "$rootdir/GMAPRESCUE" ]
then
echo " Gene $geneid has status GMAPRESCUE: mapping on the target with gmap"
eval gmap --ordered --min-identity 0.80 --min-trimmed-coverage 0.50 -n 1 -g $rootdir'/target.fasta' -f 2 $rootdir'/query.mrna.fasta' 1> $targetgff 2> $rootdir'/gmap.target.log' && rm $rootdir'/query.mrna.fasta'
elif [ -f "$rootdir/FULLPERFECTMATCH" ] || [ -f "$rootdir/FULLMATCHWITHMISSMATCHES" ]
then
echo " Gene $geneid has been mapped on the target with BLAT: next"
else
echo " FAIL TO EVAL THE ANCHORING STATUS OF GENE $geneid: rescue on whole genome"
cat $rootdir'/query.mrna.fasta' >> $unmappedMrnaFasta && rm $rootdir'/query.mrna.fasta'
fi
eval gmap --ordered --min-identity 0.80 --min-trimmed-coverage 0.50 -n 1 -g $rootdir'/query.fasta' -f 2 $rootdir'/query.mrna.fasta' 1> $rootdir'/gmap.query.gff3' && rm $rootdir'/query.mrna.fasta'
echo "3. indexing the query and target genomic"
samtools faidx $rootdir'/query.fasta' &
......
......@@ -19,9 +19,9 @@ transferType: 'first'
# FASTA of the target genome
targetFasta: 'data/Triticum_aestivum_arinalrfor.PGSBv2.1.dna.toplevel.fa'
#GMAP index of the genome for -d option
targetGmapIndex: 'ensembl_Triticum_aestivum_julius_2022-9-16'
targetGmapIndex: 'ensembl_Triticum_aestivum_arinalrfor_2023-2-17'
#GMAP index: path to the gmapindex directory, for -D option
targetGmapIndexPath: '/home/herimbert/gdec/shared/triticum_aestivum/julius/current/gmapdb/all/'
targetGmapIndexPath: '/home/herimbert/gdec/shared/triticum_aestivum/arinalrfor/current/gmapdb/all/'
##### ISBP/markers related config and parameters
# BAM file of markers/ISBPs mapped on the target genome
......
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