Hey everybody,
I tried to generate a FPKM abundance table followed by a count matrix of several paired fastq files. And I followed the protocol provided in Pertea et al (2016), Nature Protocols. I obtained a merged gtf file in which then I applied the mstrg_prep.pl perl script provided in Issue #113. I then generated the final abundance files and the readcounts of genes and I seem to get multiple gene ids as well as a MSTRG.X code for a single row and hence FPKM & read count value. I would greatly appreciate if anyone could help me. FWI, I seem to not get this error when using a referance gtf instead for the -e paramter part. Additionally I alligned my reads as strand specific, but did not include --fr or --rf options at any point during the stringtie pipeline.
Hey everybody, I tried to generate a FPKM abundance table followed by a count matrix of several paired fastq files. And I followed the protocol provided in Pertea et al (2016), Nature Protocols. I obtained a merged gtf file in which then I applied the mstrg_prep.pl perl script provided in Issue #113. I then generated the final abundance files and the readcounts of genes and I seem to get multiple gene ids as well as a MSTRG.X code for a single row and hence FPKM & read count value. I would greatly appreciate if anyone could help me. FWI, I seem to not get this error when using a referance gtf instead for the -e paramter part. Additionally I alligned my reads as strand specific, but did not include --fr or --rf options at any point during the stringtie pipeline.
Regards; Ege