Hello,
I'm very new to STAR and linux in general. In order to use Braker for gene annotation, I am trying to receive a spliced alignment using STAR. (I have PacBio data).
This is my command:
**module load STAR-2.7/STAR-2.7.5c
It finished running, the error file is completely empty and the log file shows "finished successfully".
My problem is that I don't understand where is the file I need with the spliced alignment.
I received as output this file "Aligned.sortedByCoord.out.bam" which has 2 KB in it which doesn't make sense.
And I tried to use it with braker and got an error saying the spliced alignment files are wrong.
Hello, I'm very new to STAR and linux in general. In order to use Braker for gene annotation, I am trying to receive a spliced alignment using STAR. (I have PacBio data). This is my command: **module load STAR-2.7/STAR-2.7.5c
STAR --genomeDir /dorotheeh/hadjez/genome_index/ --genomeFastaFiles /dorotheeh/hadjez/NextDenovo_pilon_sorted.fasta \ --inputBAMfile /dorotheeh/hadjez/NextDenovo_bwa.bam \ --runThreadN 4 \ --readFilesIn /dorotheeh/hadjez/Q20RNAclean_Sorted.fasta \ --outFileNamePrefix STAR_output/ \ --outSAMunmapped Within \ --outSAMtype BAM SortedByCoordinate **
It finished running, the error file is completely empty and the log file shows "finished successfully". My problem is that I don't understand where is the file I need with the spliced alignment. I received as output this file "Aligned.sortedByCoord.out.bam" which has 2 KB in it which doesn't make sense. And I tried to use it with braker and got an error saying the spliced alignment files are wrong.
These are the log files: Log_final_out.txt
Thank you in advance!