Question: Is it possible to demultiplex a run without .locs or .filter files?
gravatar for anna.benedetti
7 weeks ago by
anna.benedetti10 wrote:


I received files from a NextSeq run and was asked to analyze it, starting with demultiplexing it. However, it seems that only the .bcl and .bci files are present in the run, and there is no .loc or .filter file in the folder sent to me. As I am unsure of whether it is still possible to recover these files, I am trying to figure out if I can start the demultiplexing job without them.

I am using bcl2fastq2 and tried using the --ignore-missing-folder and --ignore-missing-positions, but either way it returns an error of "Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::inputdataerror> std::exception::what: No tiles were found to process."

I would like to know if anyone has had an experience in which they managed to do it without those files. Or should I just give up and hope that they are available somewhere?

Thank you for any kind of help.

ADD COMMENTlink modified 4 weeks ago by Biostar ♦♦ 20 • written 7 weeks ago by anna.benedetti10

It seems really strange you would be handed raw sequencing run data, let alone raw incomplete sequencing data. Sequencing facilities in general will send already demultiplexed fastq files, is there a reason you received the run files instead the fastq files?

ADD REPLYlink written 7 weeks ago by h.mon31k

You could try IlluminaBaseCallsToFastq from (GATK). But if that does not work then you should find the entire flowcell folder to process it using bcl2fastq. If you got this data from your sequence provider it is totally fair to request that they demultiplex this data for you.

ADD REPLYlink written 7 weeks ago by genomax91k

Thank you for the suggestion! I received the files from someone else, so I am not the person who is in contact with the sequence provider... Although I am considering that, since I agree that it is very weird that they received the files this way.

ADD REPLYlink written 7 weeks ago by anna.benedetti10
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