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leeju-umich / Cho_Xi_Seqscope

Seqscope codes
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align.sh if statement missing fi, outprefix to STAR dir #5

Open tonycheng521 opened 3 years ago

tonycheng521 commented 3 years ago

Hi,

I noticed two issues in the algin.sh script:

  1. You are missing the closing fi for your if statement. It will run an error if this is not added.

  2. If you only put the filename (not absolute path) for the outprefix argument, it will get output to the STAR directory. I wasn't able to find the output file, because I was expecting it to be in the current directory, and had to check the code to find it. If you can change that, it would be more user-friendly, eg. maybe instead of doing cd $seqtkpath and cd $starpath, just specify the absolute path?

Tony

leeju-umich commented 3 years ago

Thank you for your comments! Our collaborators are working on a more user-friendly version of this, so we will release the new version soon that addresses these points.

Jingyue -- please correct these in the former version if they are quick to address. Thank you!

Sincerely, Jun Hee

On Thu, Nov 25, 2021 at 9:49 PM Pin-Chung (Tony) Cheng < @.***> wrote:

Hi,

I noticed two issues in the algin.sh script:

1.

You are missing the closing fi for your if statement. It will run an error if this is not added. 2.

If you only put the filename for the outprefix argument, it will get output to the STAR directory. I wasn't able to find the output file, because I was expecting it to be in the current directory, and had to check the code to find it. If you can change that, it would be more user-friendly, eg. maybe instead of doing cd $seqtkpath and cd $starpath, just specify the absolute path?

Tony

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Jun Hee Lee, Ph.D. Associate Professor Department of Molecular and Integrative Physiology University of Michigan Geriatrics Center 109 Zina Pitcher Place, 3019 BSRB Ann Arbor, MI 48109-2200 Office: 734-764-6789 | Lab: 734-764-6795 Fax: 734-936-9220 | E-mail: @.*** https://lee.lab.medicine.umich.edu/