I have used ERCC spike-in in my RNAseq data. I have aligned my data and now I have bam files. to count the reads per gene I used htseq-count(which needs gtf file). I also have to count ERCC (I have 98 spike-in). I have fasta file of ERCCs. do you know how I can count the ERCCs?
You can filter out and count the spike sequences (and rRNA, and linker) before alingment with TagDust 2. In the following document on GitHub, I used it to detect ArrayControl spikes, but it also work with ERCC ones. For maximal accuracy, make sure to use the translated sequences available from the NIST, and not the plasmid insert sequences (see Patch ERCC spike sequences to get their real 5-prime ends. for the long story). In any case, if you use the TagDust approach, make sure your sequences do not contain common parts such as polyA tails.