I've been following the stringtie pipeline for differential expression. I'm up to the stage of
stringtie -e -B where I'm using the merged transcript file with the alignment (.bam) files to get read coverage tables.
root="/mnt/fls01-home01/mfbx3sgh/scratch" file=$root/Genome/*.bam stringtie $file -p 8 -e -B --fr -G $root/FPKM_count/stringtie_merged_samples.gtf
I keep getting the error "the input alignment file is not sorted". My bam alignment files are definitely co-ordinate sorted, and I used them in the first step of the pipeline to generate the transcript assemblies with no problems. Anyone had a similar problem?? Thanks