Hi We had a curious event here. One of our transcript that is know to be highly expressed on our disease studied came with 0 counts for all patients. We suspected that we may have a problem with alignment or primers. This gene produce 2 different proteins in alternative and traditional splicing (calcitonin and CGRP). I converted the BAM file of all patients into a FASTA through samtools, and tried to run the STAR algorithm as follow:
STAR --runThreadN 16 --genomeDir /home/user/Desktop/test/Genome --sjdbGTFfile /home/user/Desktop/test/Genome/Homo_sapiens.GRCh38.95.gtf --readFilesIn /home/user/Desktop/test/
In "test" folder i have the fasta files, in genome i have a gtf and dna_primary_assembly GRCH38. I already changed the permission to write, read and execute files in that folder "test", nothing changes.
*EXITING because of FATAL ERROR: could not open genome file /home/lemt/Desktop/test/Genome/genomeParameters.txt SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions Apr 02 13:09:27 ...... FATAL ERROR, exiting*
Maybe my problem is a bad strategy converting the BAM into a FASTA, anyone can point different alternatives?
Machine setup: 32GB Ram, ryzen 2700, Ubuntu 18.04