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View Process Hh 09

mv /data/process/Broca/Genoma/Ensamblajes/Ensamble4SffMacho/AssemblyMacho/assembly/TotalReadsMacho.fasta .

/opt/scripts/sff_extract.pl -c —min_left_clip=4 ../RawDataBroca/Genomics/Hembra/*.sff -o TotalReadsHembra

ls
TotalReadsHembra.fasta TotalReadsHembra.fasta.qual TotalReadsHembra.xml TotalReadsMacho.fasta

Formating DB

/data/process/Broca/BlastHembraMAcho
formatdb -i TotalReadsHembra.fasta -p F -o T

Making Blast

blastall -p blastn -i TotalReadsMacho.fasta -d TotalReadsHembra.fasta -e 1e-5 -o TotalReadsMacho.fastaVsTotalReadsHembra.fasta.bn.tab -v 20 -b 20 -m 8 -a 12

Extracting reads “Macho” than not hit with “Hembra”

awk ‘{print $1}’ TotalReadsMacho.fastaVsTotalReadsHembra.fasta.bn.tab | sort | uniq > IdsMachoHitWithHembra
grep ‘>’ TotalReadsMacho.fasta | sed ‘s/>//g’ | sort | uniq > IdsTotalReadsMacho
wc -l IdsMachoHitWithHembra
1227979 IdsMachoHitWithHembra
wc -l IdsTotalReadsMacho
1244500 IdsTotalReadsMacho

sdiff IdsTotalReadsMacho IdsMachoHitWithHembra | grep ‘<’ | sed ‘s/ IdsMacho_NO_HitWithHembra
wc -l IdsMacho_NO_HitWithHembra
16521 IdsMacho_NO_HitWithHembra

cdbfasta TotalReadsMacho.fasta
cdbyank TotalReadsMacho.fasta.cidx < IdsMacho_NO_HitWithHembra > ReadsMachoNoHitWithHembra.fasta
grep -c ‘>’ ReadsMachoNoHitWithHembra.fasta
16521