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Question: Can Anyone Help Me In Finding The Script That Convert .Fastq To .Fasta Format
1
gravatar for Syed Imtiyaz
8.2 years ago by
Syed Imtiyaz • 40
Syed Imtiyaz • 40 wrote:

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
fasta perl fastq conversion awk • 4.3k views
ADD COMMENT • link •
modified 7.7 years ago by Nicolas Rosewick ♦ 8.5k • written 8.2 years ago by Syed Imtiyaz • 40

http://hannonlab.cshl.edu/fastx_toolkit/

ADD REPLY • link written 8.2 years ago by Michael Schubert • 6.9k
3
gravatar for Ttnguyen
8.2 years ago by
Ttnguyen • 70
Ttnguyen • 70 wrote:

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
ADD COMMENT • link written 8.2 years ago by Ttnguyen • 70

THANK YOU IT WORKS !!!!!!!!

ADD REPLY • link written 8.2 years ago by Syed Imtiyaz • 40
2
gravatar for Nicolas Rosewick
8.2 years ago by
Nicolas Rosewick ♦ 8.5k
Belgium, Brussels
Nicolas Rosewick ♦ 8.5k wrote:

check this out : http://stackoverflow.com/questions/1542306/converting-fastq-to-fasta-with-sed-awk
ADD COMMENT • link modified 7.1 years ago by Istvan Albert ♦♦ 81k • written 8.2 years ago by Nicolas Rosewick ♦ 8.5k

THANK YOU!!!!!!!!!!!!!

ADD REPLY • link written 8.2 years ago by Syed Imtiyaz • 40
2
gravatar for pmenzel
8.2 years ago by
pmenzel • 310
pmenzel • 310 wrote:

Just did this with fastq_to_fasta from the fastx package (http://hannonlab.cshl.edu/fastx_toolkit/)
ADD COMMENT • link written 8.2 years ago by pmenzel • 310

Thank YOU !!!!!!!!!!!

ADD REPLY • link written 8.2 years ago by Syed Imtiyaz • 40
0
gravatar for Wilber
8.2 years ago by
Wilber • 0
Wilber • 0 wrote:

awk '/^@/{header=$0;getline;sequence=$0;gsub("@",">",header);printf "%sn%sn,header,sequence}' FAST-FILE
ADD COMMENT • link written 8.2 years ago by Wilber • 0

THANK YOU!!!!!!!!!!!!!

ADD REPLY • link written 8.2 years ago by Syed Imtiyaz • 40
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