Barcodes only in Read 1
ahish-sujay opened this issue · 6 comments
Hi! I was curious to know if the tool would be able to split paired-end FASTQ files that have a barcode close to the end of the read in only Read 1? I wasn't 100% sure and could not really figure it out from the documentation. Thanks!
Is the barcode in a fixed location, or is it at a variable location?
The barcode is in a fixed location. The Read1 is about 28bp in length and is always in a fixed location between the 21-26 positions. For context if needed, this is 3' RNASeq with a depth ~1 billion reads, and we're interested in Read 2 but would need the Read 1 to demux/split based on barcodes in Read1.
Would you mind re-reading the usage on how to specify read structures? And we have more verbose documentation here? https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures.
If it doesn't make sense how to specify the read structure, we'll want to figure out why, so we can improve the usage.
Oops, I completely missed that, sorry! Thank you so much, will take a look at this as to how to specify the read structure.
Was extremely easy to figure out the read structure. Was able to demux/split for my files of interest in only 30 mins compared to other ones that took me more than a few days. Thanks for all the help and sorry for not digging a little deeper into the docs!
@ahish-sujay I am glad it worked!!!