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Old 12-05-2015, 02:50 AM   #1
Avinash_dhar
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Default Ngs...roche 454

hello everyone
i am completely new to NGS analysis. I want to analyse roche 454 data which i have downloaded from ena database (in fastq format) for its quality. I have read that roche data is in *fna and *.qual format. So how do i convert this fast q data into *.fna and *.qual format................
thank you
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Old 12-05-2015, 07:27 AM   #2
mastal
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In the fastq files, the second line of each entry is the read sequence, and the fourth line gives the base qualities.
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Old 12-05-2015, 11:53 PM   #3
Avinash_dhar
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hiiiii......
if we want to convert the sra data into *.fna and *.qual format......which tool/protocol should we use......?
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Old 12-06-2015, 04:54 AM   #4
blancha
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A simple Google search will give you several tools to do the conversion you want.
For example,
http://www.bioperl.org/wiki/Converti...STA_QUAL_files

Unless you're using a specific tool that requires the FASTA+QUAL format, I see no reason to do the conversion. The FASTQ format is the most common file format to represent sequences with their quality scores, and is the standard accepted by nearly all programs.
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