Hi!
I run Stringtie on a collection, after HISAT2, with a biomart gtf file mixed with ERCC92 annotations. In optional output files for ballgown, I obtained gtf files which show FPKM values:
“|MGP_C57BL6NJ_T0001004|StringTie|exon|1|302|1000|.|.|gene_id “STRG.1”; transcript_id “STRG.1.1”; exon_number “1”; cov “5.331126”;|
|MGP_C57BL6NJ_T0000734|StringTie|transcript|1028|1373|1000|.|.|gene_id “STRG.2”; transcript_id “STRG.2.1”; cov “4.471098”; FPKM “8.614864”; TPM “11.760258”;|”
But in ‘t_data.ctab’ no FPKM values are being showed:
“|2|1|+|135861|135970|MGP_C57BL6NJ_T0099566|1|110|MGP_C57BL6NJ_G0037612|Gm26206|0|0|
|3|1|-|236101|246546|MGP_C57BL6NJ_T0019164|2|4153|MGP_C57BL6NJ_G0016197|Xkr4|0|0|”
This is not the problem with ERCC transcripts they are displaying FPKM values.
Help is much appreciated.