I am aligning some FASTQs with STAR using a custom index I created to add a few exogenous constructs to the human genome. One of these constructs is eGFP. In the Aligned.out.sam file generated by STAR, I see many alignments like this:
A00661:41:HYKT7DRXX:1:1205:19696:22733 83 eGFP 494 255 50M = 400 -144 ACTTTAAGATCCGACACAATATTGCGGACGGTTCGGTGCAGCTTGCGGAC FFFFFFFF:FFFFFF::FFF:F:F,FFFFFFFFFFFFFFFFFFFFF:F,F NH:i:1 HI:i:1 AS:i:95 nM:i:1
However, the count for eGFP in ReadsPerGene.out.tab is zero:
ENSG00000268674 0 0 0 eGFP 0 0 0
The corresponding entry in my customized GTF is:
eGFP ensembl exon 0 717 . + . gene_id "eGFP"; transcript_id "eGFP"; exon_number "1"; gene_name "eGFP"; transcript_name "eGFP";
Other genes and constructs seem to be counted fine. Can anyone spot what the problem is or give some direction as to how to investigate further?