Problem with twopassMode Basic

[Matthew Jones]

Hello,

I'm using Star 2.4.2a and I have been unsuccessful in using the twopassMode with my alignments. We are using RNA-seq data and are aligning to the m38.p4 genome. My command line input is;

star --runThreadN 16 --genomeDir StarGRCm38.p4 --readFilesIn BMDM.Z6/WTclipped.fastq --outFilterMismatchNmax 3 --outSAMtype BAM SortedByCoordinate --twopassMode Basic

Star will not initiate and I receive the following error message;

EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "twopassMode" in input "Command-Line-Initial"

SOLUTION: use correct parameter name (check the manual)

Do you have any advice on how to address this?

Thank you for your time

Matt

[Alexander Dobin]

Hi Matthew,

please make sure that you are using the 2.4.2a version of the STAR, the first line of the Log.out file contains the version.

If that's the case, please send me the Log.out file.

Also, if you are generating the genome without annotations, please use the latest patch from GitHub master (for both genome generation and mapping) - it has a bug fixed that may cause problems.

Cheers

Alex