mapping Viral genome output SJ.out.tab with splice junctions and not reads per gene

[zeryas]

Hi Alex,

I am trying to map RNAseq data from infected specie to a viral genome, so i generated my genome index without annotation and then did the mapping, i get an SJ.out.tab with 9 columns that are described in the manual, here is an exemple :

CY088 19 714 1 1 0 3 0 18 CY088 27 714 1 1 0 71 1 26 CY088 183 312 1 1 0 2 0 12 CY088 201 254 0 0 0 8 0 74 CY088 250 653 2 2 0 2 0 46

my question is : how can i get reads per gene instead of splice junctions cause i am just intresed in seeing if the viral genome is present and in which quantity, what parameters should be included in order to get that result ?

Thank you

[alexdobin]

Hi YasmineZ,

for reads-per-gene quatification, you need to use --quantMode GeneCounts option, provided that your GTF file has gene_id for each exon.

[zeryas]

Hi Alex,

Thank you for your answer, but i did not use annotation file for my viral genome, all i want to see is that if there is an enough amount of viral genome in the sequenced samples i have, is there any parameter for that ?

Thank you

Yasmine

[alexdobin]

Hi Yasmine,

if you want to count reads per gene, you need to use annotations. Otherwise STAR will not know where the genes are in the genome.