Good morning everyone,
I found data from GEO, GSE115469, and the author stated that it is in a paired fastq layout. However, I have only found one fastq file. I am wondering how to handle this fastq file because I need to re-run the cell ranger process.
Thanks Andy
If you're dealing with bulk data (technically possible even in single cell data), Paired End reads can also be interleaved and stored in a single FASTQ file. Always examine file content - that's part of the sanity check.
That would be unusual, since this is single-cell data.
OP's post does not mention single-cell, which is why I suggested this possibility. For future users that might run into this problems, I think it's important to understand that number of files may not be the most reliable indicator of SE/PE nature of sequencing.
GEO accession listed in original post is for single cell dataset.
I initially didn't bother looking up the GEO entry. I assumed it was bulk so the option did not cross my mind. I'll move my answer to a comment. I wish OP would have mentioned it - if I assumed bulk, so might other people that actually run into this problem in the bulk context.