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Can Anyone Help Me In Finding The Script That Convert .Fastq To .Fasta Format

can anyone help me in finding the script that convert .fastq to .fasta format it would be help full if the script would be in perl scrpt or awk

conversion fastq fasta perl awk
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updated by Nicolas Rosewick Nicolas Rosewick • written by Syed Imtiyaz • Syed Imtiyaz

4 answers

How about this?

awk 'BEGIN {id=1; seq=2;} NR==id{ sub(/^@/,">",$0); print $0; id += 4;} NR==seq{ print $0; seq += 4}' FASTQ_FILE

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written by Ttnguyen • Ttnguyen

check this out : http://stackoverflow.com/questions/1542306/converting-fastq-to-fasta-with-sed-awk

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updated by Istvan Albert Istvan Albert • written by Nicolas Rosewick Nicolas Rosewick

Just did this with fastq_to_fasta from the fastx package (http://hannonlab.cshl.edu/fastx_toolkit/)

• 1 views • link
written by pmenzel • pmenzel

awk '/^@/{header=$0;getline;sequence=$0;gsub("@",">",header);printf "%sn%sn,header,sequence}' FAST-FILE

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written by Wilber • Wilber

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