STAR output files

[Gimena Alegre]

Hello,

I understand that STAR has the ability to output alignments in SAM format or BAM (using --outSAMtype BAM SortedByCoordinate for example) and the default output format is SAM. But is there a way to output both (SAM and BAM) files in the same run?

Thank you for your help!

Gimena

[Alexander Dobin]

Hi Gimena,

SAM and BAM cannot be output at the same time, but you can always convert them into each other with samtools view command.

Cheers

Alex