Hello,
I have 250 bps paired end illumina sequencing reads with UMIs. I am interested in identifying splice junctions using my data.
I have used STAR in the past for non-UMI runs and was interested in the junctions.out file. Is there a way I can incorporate UMIs into STAR? ( I think right now one can only do it using STARsolo for single cell, so not useful for me).
Another method I can think of is use UMI-tools and extract UMI barcodes, then use STAR and then remove duplicates from the aligned file and then somehow look at splice junctions. But I am hoping for a more intuitive solution to this problem.
Thanks!
Edit: I tried running STAR ( --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical) by both extracting UMIs and adding them to the read name and aligning the reads to my reference and also by simply aligning reads to reference (without adding UMIs to the read name). I however see the same number of aligned reads in both cases. This makes me believe that this method of using barcodes to identify splice junctions might not work out. Please correct me if I am wrong.
