I have Illumina paired end reads miRNA seq data (which I did not generate) that I need to analyze. Evaluating the fastq file, 3' adaptor of sequence, 12 base UMI, RT primer sequence and universal adaptor of unknown length is only on the R1 not R2.
When I run umi_tools extract for paired end, only the R1 get extracted and not R2.
I have no idea how the library was made or the kit used.
I have looked at an earlier posting here [umi_extract paired end][1] [1]: UMI_extract for paired end reads of micro_RNA I got lost at the response of @iansudbery. Actually mine is exactly the same as the one described previously. Someone with information how they dealt with such.
If I use only 1 of the pairs (as in R1 alone) will it gravely affect the outcome? Have seen elsewhere where they say as single seq of the pair is enough.
It is not clear what the issue here is, and it would hep immensely if you would also provide the code you tried.
This is also super bad, you should know how the data is structured so to know how to deal with it.
If I had to take a guess, I would say R1 has the barcode information and R2 has the actual miRNA sequences. You only need the R1 reads to extract the barcode, which umi-tools does and places them into the R2 read.