make.sra for sff question

Commands in mothur
1

I used make.sra to prepare sff and xml files for SRA submission.
I have 2 questions:

  1. Do you recommend using the same pdiffs and bdiffs as for my analysis? On my first go I just left the defaults but maybe I should change this.
  2. The xml output included the .scrap.sff files (these were not in my mimark files) -is there a way to avoid this? The SRA would like it out of the xml or they would like the .scrap.sff file which I don’t think I want to submit.
    Thanks!
2
  1. Do you recommend using the same pdiffs and bdiffs as for my analysis? On my first go I just left the defaults but maybe I should change this.

Yeah, i would use the same pdiffs/bdiffs

  1. The xml output included the .scrap.sff files (these were not in my mimark files) -is there a way to avoid this? The SRA would like it out of the xml or they would like the .scrap.sff file which I don’t think I want to submit.

Let me have Sarah get back to you on this one…

3

Thanks for the feature request! We will add making scrap sequence submission optional to our list. If you send me your xml file I can remove the scrap references for you, mothur.bugs@gmail.com.