Is there a way to overwrite the STAR parameter --outSAMunmapped ?

[TatevikJ]

I don't want to have unmapped reads included within the output bam, so I specify these STAR parameters in yaml file:

additional_STAR_params: '--outSAMunmapped None --limitSjdbInsertNsj 2000000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq CTGTCTCTTATACACATCT CTGTCTCTTATACACATCT'

However, I get this error:

EXITING: FATAL INPUT ERROR: duplicate parameter "outSAMunmapped" in input "Command-Line"
SOLUTION: keep only one definition of input parameters in each input source

Is there a way to overwrite the STAR parameter --outSAMunmapped ?

[cziegenhain]

Hi,

This is not intended for zUMIs and skipping the unmapped reads output during zUMIs may disrupt correct generation of statistics within zUMIs. I recommend that you remove unmapped reads from the bam file using samtools after zUMIs is completed.

Best, Christoph

[TatevikJ]

Thank you for your prompt response.

Regarding the unmapped reads, I would like to confirm if they have any additional purpose or if they are used in any other way within the analysis pipeline, aside from the generation of statistics.

[cziegenhain]

Apart from statistics, they are used for ensuring the accuracy of the downsampling feature. Other than that unmapped reads are just kept for not discarding observed data.

[TatevikJ]

Ok, thank you!