Hello ALL! Hope you are having a great new years so far!
I am back again with a question & would be delighted if I can have some help or suggestions (:
I am trying to merge a transcript but it is giving me a few errors. First I want to say that I HAVE tried a few times before posting to this website
1) tried deleting all uploaded codes/software then I re-installed all programs back on using terminal. The codes included the following:
- Hisat2 https://anaconda.org/bioconda/hisat2
- samtools https://anaconda.org/bioconda/samtools
- stringtie https://anaconda.org/bioconda/stringtie
- gffcompare https://anaconda.org/bioconda/gffcompare
2) The professor I am taking the class with provided a transcript for us to follow. I followed it to the T, w/o using any paths unless instructed. That codes is:
stringtie --merge -G paeruginosa.gff -o stringtie_merged.gtf assemblies.txt
3) Unfortunately it gives me 2 error msg, which are
Error: cannot find file 'stringtieout/ film_01.transcripts.gtf' and assemblies.txt does not look like GFF!
Any suggestions on how to fix this?
Thank in advance (: