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alexdobin / STAR

RNA-seq aligner
MIT License
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Output of STAR #2018

Open RacheliHadjez opened 9 months ago

RacheliHadjez commented 9 months ago

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!

alexdobin commented 8 months ago

Hi @RacheliHadjez

For long reads (HiFi PacBio) you could use STARlong. However, I recommend using minimap2.