Hi, I am running some RNAseq analyses, but I have the problem of not having a .gff/.gtf file. Here is my analyses pipeline:
- mapping with Bowtie2 (without providing .gff reference)
- assembly with Cufflinks
- merging with Cuffmerge the transcript.gtf files of all my samples (output of Cufflinks)
- counting with HTSeq-count using the files.SAM (output of Bowtie2) and the merged.gtf (output of Cuffmerge) proceeding with DESeq then.
I would like to use HTSeq/DESeq and this is the only way I found to overcome my problem of not having a suitable .gff/.gtf file. Is it this an acceptable pipeline?