Question: Combining FASTA and Qual files to generate FASTQ
gravatar for olivermj
2.9 years ago by
olivermj0 wrote:

I am trying to combine a .FASTA file with a .QUAL file using the tool provided under "NGS: QC and manipulation" - I am loading local files and it appears to run - however it does not produce a FASTQ file and says that no qual scores were added to the sequences - seems it sees the fast file but does not read the .qual file - there is no explanation as to what the problem could be so I cannot troubleshoot the process to see if I can fix it - any help would be helpful!

software error • 1.2k views
ADD COMMENTlink written 2.9 years ago by olivermj0

Hello - Are you working on a local or at or somewhere else? Share URL if other. Thanks! Jen, Galaxy team

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson25k

I was working on - the program worked once I ignored the addition of the .qual file - the program created "fake" quality scores for each of the sequences and this has allowed me to progress. I guess it did not like using the .qual file I provided.


ADD REPLYlink written 2.9 years ago by olivermj0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello again,

Thanks - that helped to focus on the ways we can help you through this. 

First, double check that the quality score file was completely uploaded. If the data is over 2 GB or your connection is slower, use the FTP upload method. Using an FTP client (unless you are comfortable with the command-line) is a simple way to track upload success. It is possible that the data was corrupted prior to loading into Galaxy (via prior data transfers), but this is a start. You can check that the two datasets of similar size locally. 

Next, what is sequencing technology is the data based on? I am guessing not Illumina, but that could be an incorrect assumption. has more details for working with Illumina data (the primary type accepted by tools on the main instance). An intact fastqsanger dataset is required for Grooming, which is not possible yet given the current state of the data, but source details will stll help.

You can answer here, or better, include the answers in a bug report submitted using the green bug icon. If you are unsure of some, we can check most of that when reviewing the data (specifically the data type, successful upload double checks are limited on our side, but some is possible). Make sure that all relevant datasets are undeleted and please include a link to this post. 

If you uncover the issue yourself, please share back that this is resolved if you have time.

We are catching up on helping users on detailed cases like this, but expect to reply to most within the next day, maybe two.

Sorry for the problems and we appreciate your patience for support replies after the US holidays!


ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson25k
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