How to extract the shortest and the longest isoform from Trinity.fasta file?
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5 weeks ago
FadyNabil ▴ 10

I have a Trinity.fasta file an I want to extract the shortest and the longest isoform from it

assembly fasta trinity • 193 views
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Entering edit mode
5 weeks ago

Hey,

samtools faidx Trinity.fasta # create an index to get the length of each sequence (length values are stored in the second column of the Trinity.fasta.fai file)

awk 'BEGIN{getline; min=$2;max=$2}
            {(min>$2)?min=$2:"";(max>$2)?"":max=$2}
       END{print min, max}' Trinity.fasta.fai # print the max and min values in the second column of  the Trinity.fasta.fai

#201 2114

awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' < Trinity.fasta > linear.fasta # linearize the Trinity.fasta
cat linear.fasta | grep -A1 'len=201' --no-group-separator > sequences_201.fasta # get the shortest sequences using the field 'len=###' in the fasta header
cat linear.fasta | grep -A1 'len=2114' --no-group-separator > sequences_2114.fasta # get the longest sequences using the field 'len=###' in the fasta header
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