Question: Can Anyone Help Me In Finding The Script That Convert .Fastq To .Fasta Format
1
gravatar for Syed Imtiyaz
7.5 years ago by
Syed Imtiyaz40
Syed Imtiyaz40 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 • 4.1k views
ADD COMMENTlink modified 7.0 years ago by Nicolas Rosewick7.4k • written 7.5 years ago by Syed Imtiyaz40

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

ADD REPLYlink written 7.5 years ago by Michael Schubert6.9k
3
gravatar for Ttnguyen
7.5 years ago by
Ttnguyen70
Ttnguyen70 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 COMMENTlink written 7.5 years ago by Ttnguyen70

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

ADD REPLYlink written 7.5 years ago by Syed Imtiyaz40
2
gravatar for Nicolas Rosewick
7.5 years ago by
Belgium, Brussels
Nicolas Rosewick7.4k wrote:

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

ADD COMMENTlink modified 6.4 years ago by Istvan Albert ♦♦ 79k • written 7.5 years ago by Nicolas Rosewick7.4k

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

ADD REPLYlink written 7.5 years ago by Syed Imtiyaz40
2
gravatar for pmenzel
7.5 years ago by
pmenzel310
pmenzel310 wrote:

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

ADD COMMENTlink written 7.5 years ago by pmenzel310

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

ADD REPLYlink written 7.5 years ago by Syed Imtiyaz40
0
gravatar for Wilber
7.5 years ago by
Wilber0
Wilber0 wrote:

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

ADD COMMENTlink written 7.5 years ago by Wilber0

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

ADD REPLYlink written 7.5 years ago by Syed Imtiyaz40
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