I have been following the procedure given in the paper "Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown" with my own examples of course.
1) I have sorted the SAM files to BAM just fine with no errors.
2) Then I assembled transcripts for each of my samples following the example:
stringtie -p 8 -G chrX_data/genes/chrX.gtf -o ERR188044_chrX.gtf –l ERR188044 ERR188044_chrX.bam
Below is what I used for my samples:
stringtie GG1_hisat.sorted.bam -o GG1_hisat.sorted.gtf -m 300 -p5
I did not use the
-G option because I don't have a reference annotation file yet.
3) Then I merged the transcripts of all my samples:
stringtie --merge -o stringtie_merged.gtf gtf_files.txt
4) Now, I want to create a table of counts so that I can move on to use Deseq2 but I am unable to do so, and I am not sure why... maybe because I have not provided the
stringtie –B -p8 -G stringtie_merged.gtf -o ballgown_Ceratodon.gtf
input file –B cannot be found!
stringtie -p8 -G stringtie_merged.gtf -o ballgown_Ceratodon.gtf
no input file provided!