Commit 646f8aec authored by khalid's avatar khalid
Browse files

Force the order of transcripts in /tmp/ALL_transcripts.ctgs

parent d524750f
...@@ -115,6 +115,9 @@ echo ...@@ -115,6 +115,9 @@ echo
esac esac
echo -e "\nIndex built : $out/$toolidx\n" echo -e "\nIndex built : $out/$toolidx\n"
refseqALL=$out/ALL_transcripts.ctgs
echo '' > $refseqALL
#for (( j=0; j <i; j++ )) #for (( j=0; j <i; j++ ))
for ref in "${orders[@]}" for ref in "${orders[@]}"
do do
...@@ -128,10 +131,11 @@ echo ...@@ -128,10 +131,11 @@ echo
Seqlength = length($2) ; Seqlength = length($2) ;
print a[1]"\t"Seqlength > refseqs print a[1]"\t"Seqlength > refseqs
}' $out/$ref".fasta_mod" }' $out/$ref".fasta_mod"
# regroup all samples
cat $out/*.ctgs >> $refseqALL
done done
# regroup all samples
refseqALL=$out/ALL_transcripts.ctgs
cat $out/*.ctgs > $refseqALL
# mapping successively every read sets on all transcripts. # mapping successively every read sets on all transcripts.
#for (( k=0; k <i; k++ )) #for (( k=0; k <i; k++ ))
......
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