GFFCompare ".tracking" file has zero value in<FPKM>|<TPM>|<cov> columns

gpertea / gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

MIT License

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GFFCompare ".tracking" file has zero value in<FPKM>|<TPM>|<cov> columns #93

Open Miracle-Yao opened 1 month ago

Miracle-Yao commented 1 month ago

Hello, When I compared single merged.stringtie.assembly.gtf (generated by stringtie merge function) file with known annotation gtf file, I found each line in .tracking has zero value in || columns，how can I got this information? An example:

qJ:<gene_id>|<transcript_id>|<num_exons>|<FPKM>|<TPM>|<cov>|<len>
q1:MSTRG.1|MSTRG.1.1|3|0.000000|0.000000|0.000000|3357

Thanks

santataRU commented 2 days ago

Hi Yao,

I have the same issue as you. I used Gffcompare to identify novel transcripts between my cell-type-specific (HT-1080 cells) GTF annotation (generated by StringTie merge) and the hg38 GTF annotation from Ensembl. My FPKM and TPM columns show zero values. This makes sense, as we only provided two GTF annotations as input, and since FPKM and TPM information is not included in these files, the tool cannot compute these values.

Xiao