Does hisat2 –rg flag eat the “/” character in multiline definitions?
Hello, I am trying to use hisat2, but I noticed something weird.
When running it like so:
hisat2
-p 8
--rg-id=UHR_Rep2
--rg SM:UHR
--rg LB:UHR_Rep2_ERCC-Mix1
--rg PL:ILLUMINA
--rg PU:CXX1234-TGACAC.1
-x $RNA_REF_INDEX
--dta
--rna-strandness RF
-1 "$RNA_DATA_DIR/${SAMPLE}_1.fastq.gz"
-2 "$RNA_DATA_DIR/${SAMPLE}_2.fastq.gz"
-S ./sams/UHR_Rep1.sam
I would get this output on the commandline:
(ERR): hisat2-align exited with value 1
./align_command.sh: line 16: --rg: command not found
./align_command.sh: line 17: --rg: command not found
./align_command.sh: line 18: --rg: command not found
./align_command.sh: line 20: -x: command not found
I thought this was pretty strange, and after mucking about I tried this, and it worked!
hisat2
-x ./$RNA_REF_INDEX
--dta
--rna-strandness RF
-1 $RNA_DATA_DIR/${SAMPLE}_1.fastq.gz
-2 $RNA_DATA_DIR/${SAMPLE}_2.fastq.gz
-S ./sams/UHR_Rep1.sam
--rg-id=UHR_Rep2 --rg SM:UHR
My question is does –rg actually eat up the “” character? Is that why I was getting the command not found error? If so, how can I ask it to not act like this?
• 9 views
Read more here: Source link