Help bcl to fastq
Hello,
I am new to bioinformatics, our NextSeq500 produces the bcl and I want to convert only 001 to fastq; When I write the command "bcl2fastq --runfolder-dir ... --output-dir ..." it shows me the error "unabel to find bcl file 002"
Can you help me.
Thank you.
(je parle français)
1 answer
Assuming you are using the correct options for other things you could try --ignore-missing-bcls option. This will use N/# for missing calls. If you need more specific help then post your actual bcl2fastq command and the exact error (you can remove actual file/directory names).
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when I copy all my files bcl it works when I want to do one of my samples I do not know how to do, I will try your method thank you on the other hand I will have another question when I put my command line bcl2fastq -R <xxx> -o <yyy> it makes me all the bcl in one go I would like to do it in a targeted way Once I have my fastq it passes automatically to the sample 2 the time that I analyze the sample 1 ...
Thank you
Please use
ADD COMMENT/ADD REPLYwhen responding to existing posts to keep threads logically organized.If I understand what you are saying then I would advise that you wait for the entire process to complete before touching the sample files in the demultiplexed (
unaligned) directory. Since you have a single pool, all samples files are potentially being written to as the data is demultiplexed. I also suggest that you use--no-lane-splittingoption to get a single file per sample (instead of 1 per lane).what I want is to be able to pass my sample after another, because when I run the command bcl2fastq he passes them all 12 samples in one moment is seen that it is exom it is heavy
You could put just one sample in the samplesheet, run
bcl2fastqand extract the data for that one sample. Then repeat the process for remaining 11 for 11 times. I am not sure why you would want to do this since this would be inefficient.Am I misinterpreting what you are saying above?
Thank you for your answer
what I want exactly is to pass the other 11 automatically I think I'll try with the 1st suggestion :) peux tu m'aider pour les autre ligne de commande depuis le fastq jusqu'au VCF
Thank you so much