Hello,
This may be a very elementary question but since what I have found thus far on the internet has not entirely clarified this for me, I figured I'd ask here.
When a sequencing experiment is run on an Illumina platform, after demultiplexing, there are always *_Undetermined.fastq.gz files. I am lost as to why exactly some reads end up in there, and what the purpose of this file is. I've read that sometimes one may use this file to observe index frequencies or for other troubleshooting issues, but again, I am not entirely clear on this. Is the presence of this file strictly for troubleshooting (i.e. the reads in this file will never be used in any downstream analysis)??
Thanks in advance for any help on this.
This may be a very elementary question but since what I have found thus far on the internet has not entirely clarified this for me, I figured I'd ask here.
When a sequencing experiment is run on an Illumina platform, after demultiplexing, there are always *_Undetermined.fastq.gz files. I am lost as to why exactly some reads end up in there, and what the purpose of this file is. I've read that sometimes one may use this file to observe index frequencies or for other troubleshooting issues, but again, I am not entirely clear on this. Is the presence of this file strictly for troubleshooting (i.e. the reads in this file will never be used in any downstream analysis)??
Thanks in advance for any help on this.
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