I sent for targeted 250x2 NGS some pooled amplicons. The company did enzymatic barcording for their platform so I got two files (read1 and read2) out of which I extracted my barcoded samples. Till here all good. However, I have reads for the same directions in both read 1 and read 2, so I ended up with 2 files per samples per read. Now, I need to concatenate/merge/pool them. To do so, I used the Concatenate datasets function. However, when loading these concatenated samples on CRISPResso2 (I need to analyze editing efficiency), the run always fails due to some merging problem. I assume the problem is in the concatenating as if I upoload the single files individually, CRISPResso2 works fine. Anybody can help with this?
What is the error? Search this site with “sharing your history” if you are not sure what we’ll need for troubleshooting: either the actual history or the same technical details for input/output in screenshots, etc.
If you didn’t confirm the format was intact after uploading (FastQC or Fastq Info are common choices), please double check that first.
If you are treating reads labeled as forward/R1 and reverse/R2 as both being “single end” in a single file … some tools may complain, and there is probably another way to use the tool (possibly explained on the tool form help section, or tutorial links). But do share your details if that doesn’t seem to be what is going on.
Let’s start there.