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I am trying to do assembly and the file format is .qual format. I have tried geneious and velvet format but they dont support .qual format, so I have tried to convert this file into fasta file and then performing the assembly. Geneious and velvet both accepting the file now but I am getting message that "NO CONTIGS IS FOUND" by geneious and contig file is empty in case of velvet. I dont know where I am doing wrong please reply me...
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Last edited by paa6; 02-03-2014, 04:49 PM. -
Is this data from Illumina sequencing? Illumina data has been in FASTQ format (with some changes to the way the quality values were encoded) over the years.
Can you post a small example from a file you are referring to as being of .qual format? -
ACTUALLY MY FILE IS IN .QUAL FORMAT...i guess in this file format sequnce is in numeric format...this is the file i have got from my PI. there is other file also in .sff format but first he wants to assemble .qual format file.
one thing I have understood while using geneious that u should have forward and reverse reads to perform assembly but in my case I have only one read file so I dont know how to assemble it...Comment
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You appear to have data from a SOLiD sequencer. I have no experience with data from a SOLiD instrument. Hopefully someone else on the forum will step in to help.
Meanwhile see some past threads related to this topic:
Last edited by GenoMax; 02-02-2014, 06:46 PM.Comment
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THANK U SO MUCH...but is this mean that my sequence is not illumina sequencing?? then what kind of sequence is this..I mean what should I call it...I am looking for a name..Comment
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Well, it seems that you have a Roche 454 dataset. The "qual" file is only the quality portion of the dataset (missing the fna = sequence file). The "original" or "raw" file, containing all sequence information is the SFF file you have mentioned.
So either ask your PI to also provide the corresponding fasta (fna) sequence file or just create your sequence files by yourself from the SFF file using public available tools (sff_extract, SFF Tools from Roche).
But AFAIR "geneious" can directly import SFF files, which should get the most out of the data (and is probably the safest way).Comment
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I guess this could also be a 454 data set (though why paa6 was not given the *.fna files is a mystery).
@paa6: In any case you should get additional information about this data set from your supervisor. At the least start with the SFF files and see if Geneious can import them.Comment
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i have only two types of files .sff and .qual format. After reading so much now I am also thinking that this is 454 sequencing files...I have tried to import .sff into geneious but it's showing error message.Comment
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this is the msg I am getting...Comment
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Try getting the sequences from the sff file using sff_extract.
You can also convert the sff files to a text format, .sff.txt, so then you could have a look
at the first few lines to see if the data looks like it is what you expected.
I'm not sure if sff_extract or seq_crumbs will do that, though, or if you need the Roche software.Comment
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Your dataset seems to be incomplete (missing fna, basic stats) .. ask your PI for information about the data and the complete dataset (fna/qual and sff file(s)).
How did you receive your data? USB stick/disk, download?
If it is a big SFF file you might want to check MD5 checksums (in case you have downloaded the data).
Concerning the error you get during import into geneious you should contact their support team.Comment
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@mastal I did try to change into .txt but sadly its not responding...not getting open...so I will try ur link...thanks...Comment
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@sklaegs I got my data from usb and that was given by my supervisor...Comment
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@skladge can u provide me any research paper mentioning that to assembl the 454 u need all these formats...so that I can show him proof. He was telling me that .qual is an Illumina sequencing file and .sff is 454 sequencing. So, obviously if i will try to explain him that they both are the same file of 454 sequencing and I need additional files too...so, I need to show him research paper...Comment
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Can you try to explain a bit more in detail? What did you do and what did not respond?Originally posted by paa6 View PostComment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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