I'm now 6 months into the field of NGS and analysis of sequencing data. I have been working on RNA-Seq data and recently, just started to venture into CAGE-Seq data.
I wanted to ask how do we actually map CAGE-Seq data? We did a paired-end sequencing for the CAGE data and then got the fastq files. After cleaning, I got the clean reads files for read1 and read2 but both of them are of different size. When I run them on STAR, it said that mapping could not be done as the run finished for 1 read while the other 1 is still not.
Is this normal for CAGE-Seq data? Or should we just map read1 only as we are only interested in the TSS i.e. reads seq from 5' end?
I am a bit confused how to process CAGE data here.
Please give some guidance & advice. Thank you very much.