I noticed a slight STAR command inconsistency between the website and github?

[bshaun]

Hi!

I was checking the website AMP-PD Transcriptomics Data where it is mentioned the way arguments passed onto STAR. It seems to me the command is a little different on how STAR is executed as mentioned on the Github-WDL

It could be that I am looking at the wrong url?

The difference is not much except for:

1. –chimOutType (instead of WithinBAM it is Junctions)
2. –outSAMtype (instead of SortedByCoordinate it is Unsorted)

It seems to me the github one is way it has been used since most of the alignment do have a chimeric junction file.
I just wanted to bring it to the attention of the community.

[gginnan]

Hi @bshaun, thanks for your message! Wondering if other community members who work with AMP-PD data would be able to provide insight?

@ehutchins @Rasaholiarison @mchaparro @mengxi.yang @TugceGulD @gdp22 @vdardov @ViniciusCrr

[ehutchins]

Hi @bshaun ! Thank you for bringing this up. I can confirm the github is the command that was run with:
–chimOutType Junctions
–outSAMtype BAM Unsorted

I was on the team that had discussions about the options here and we choose those intentionally to 1) output the SJ.out.tab junction file from STAR and make that available and 2) because it is less intensive computationally to sort the BAM with samtools after STAR is complete than to do it within STAR.

Thank you for bringing this up. I will email the team that manages the AMP PD website and ask them to update it.

[bshaun]

Thank you so much for the clarification! Great.

[bshaun]

Thank you so much for tagging the community members. Really appreciate it and I got the clarification needed.

[ehutchins]

Of course! I was kind of excited that it hit my niche knowledge that I could answer readily!