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Old 06-16-2014, 06:49 AM   #1
MikeT
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Default Weird quality issue

Dear all,
I just started working on an Ion Proton de novo genome sequencing project. Our service provider sent us the .fastq file, and, as I try to load it either onto Newbler or CLC Workbench (as somebody suggested me), both programs end up warning me about problems with the file.
CLC Genomics Workbench fails to import the file, warning me about an "unexpected end of file."
Newbler loads it, but, as I start assembling, it warns me about the presence of lots of sequences with long names, which renders them useless.
Only MIRA seems not to care about anything, and starts assembling.
I think the issue might be related to the quality data, since converting it to a simple .fasta file makes everything work very fine. Am I right? Have you already experienced such a problem?

-MikeT
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Old 06-16-2014, 07:58 AM   #2
GenoMax
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Is there any sort of cross platform (PC/Mac/Linux) transfer of files involved? Did you get the files on a disk or were they download from the provider (via a web link/ftp)?
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Old 06-16-2014, 08:01 AM   #3
MikeT
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Quote:
Originally Posted by GenoMax View Post
Is there any sort of cross platform (PC/Mac/Linux) transfer of files involved? Did you get the files on a disk or were they download from the provider (via a web link/ftp)?
We had to transfer the files via FTP.

-MikeT
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Old 06-16-2014, 08:06 AM   #4
GenoMax
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I wonder if they were somehow corrupted during transfer (may want to try a binary format transfer as an alternate).

Can you try to open the files in FastQC (http://www.bioinformatics.babraham.a...ojects/fastqc/) to get a general idea about quality of data contained within these files (and to see if FastQC complains about the file format)?
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Old 06-16-2014, 09:09 AM   #5
MikeT
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Yes, I managed to open it up with PRINSEQ, and it didn't complain about the format; also, quality scores ranged up to about 25, which shouldn't be that bad for Ion Torrent. However, FastQ Groomer on Galaxy couldn't handle the file and ended with an error. If you wish, I can try to post the first sequences and related quality scores tomorrow.

-MikeT
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