Read mapping problem with STAR

Question

[Ricky]

I have previously used hisat2 for mapping RNA seq reads but I now would like to try STAR as an alternative. Generating the index for the Arabidopsis genome wasn't a problem but when I use the command below for mapping of my single end reads, it appears that I only get the content of my fastq.bz2 file on standard output.

$ STAR --runThreadN 8 --genomeDir ~/exp_run/STAR --sjdbGTFfile ~/exp_run/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf --readFilesIn ~/Priming/data/Col0C1_R1_nonrRNA.fastq.bz2 --outFileNamePrefix Col0C1.star. --readFilesCommand bzcat --outStd SAM

This goes on for ever and I terminated the job after approximately 3hrs (hisat only takes about 15 mins to map the same fastq.bz2 file). Can anybody spot any problems in my command? Thanks

Answer 1

[GenoMax]

You are using --outStd SAM which is causing the alignments in SAM format to be sent to STDOUT (screen).

[Ricky]

Left that bit out. Worked, thanks.

[GenoMax]

You can accept the answer by using green check mark then.