Are SAM attributes necessary if I only keep the BAM files using STAR?

Question

[ev97]

I am trying to understand some parameters of the tool STAR and I am wondering if I should add some parameters or not.

If I just keep the BAM files using --outSAMtype BAM Unsorted, does it make sense to add some parameters related to SAM, such as --outSAMattributes, --outSAMattrIHstart or --outSAMunmapped? Will they be kept in the BAM files?

I saw some script where BAM files were kept but those commands were also added, and I don't know if the BAM file will contain the selected choices of the SAM file or not, cause although I am reading what the parameters do, as I don't know how to see the results, I don't know if I should choose them.

Any help will be welcomed.

Thanks in advance.

[GenoMax]

If you check STAR manual : you will see that section 4.2.2 deals with --outSAMattributes. If you have a need for the attributes implemented then you will have to use that option. If you have so far not needed them then you probably don't. outSAMattrIHstart is required by cufflinks/stringtie. If you don't use those programs then you don't need those attributes. outSAMunmapped is going to generate a file with unmapped reads in SAM format. If you don't need that then don't use that parameter.

[rfran010]

It also seems like there maybe be some confusion on the SAM/BAM relationship.

The outSAM parameters should apply to both the SAM output and the BAM output, since the BAM output is the binary version of the SAM output. However, the outBAM parameters may be the specific options that can only apply to the BAM output.

So if you use the options you specify, they will be kept in the BAM files.