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Old 11-17-2010, 02:21 AM   #1
ketan_bnf
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Location: India

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Default Help needed for fastq format

Hi all,

I have 454 *.sff file and successfully converted it into *.fasta and *.qaul using PyroBayes.

From these *.fasta and *.qual files i am generating *.fastq file by a perl script fastaQual2fastq.pl, but when i try to run MosaikBuild, it gives error : can not open FASTQ file, integrity check failed.

Why? Pls help me.


I have attached perl file with this.

I am running Mosaik on ubuntu 9.10.
Attached Files
File Type: pl FASTA_QAUL to FASTQ.pl (965 Bytes, 11 views)
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Old 11-17-2010, 03:16 AM   #2
maubp
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You could try using sff_extract to convert SFF to FASTQ. It defaults to doing SFF to FASTA+QUAL, but the -Q or --fastq switch changes that.
http://bioinf.comav.upv.es/sff_extract/index.html
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Old 11-17-2010, 05:15 AM   #3
kmcarr
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Ketan,

You are using a buggy version of the script. If you read further down in that thread you would see that a bug was identified and patched version of the script was posted.

http://seqanswers.com/forums/showpos...2&postcount=17
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Old 11-17-2010, 06:55 PM   #4
ketan_bnf
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Thank You very much for your replies
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