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Gregor-Mendel-Institute/nanoPARE
Installation troubles

Hi, Thank you for all the effort you have put into this technique and the code. I have unfortunately run into a few issues with installation. I ran installation with your annotation and genome files (containing ...
  • satyakiprv
  • 9
  • Opened 
    on Jun 12, 2019
  • #7

Gregor-Mendel-Institute/nanoPARE
setup failure with custom genome / STAR index fail?

Hi again Michael, really sorry to keep posting things, but I think I have another bug (or anyway something I can t work through myself). First time I tried to run ./nanoPARE_setup.sh with my own genome ...
bug
  • MikeAxtell
  • 4
  • Opened 
    on May 2, 2019
  • #6

Gregor-Mendel-Institute/nanoPARE
EndCut documentation

Hi again Michael, This is also an enhancement request / comment: More detailed documentation on how to use EndCut would be welcomed. As it is in the README that actual usage of this step is not described. ...
  • MikeAxtell
  • Opened 
    on May 2, 2019
  • #5

Gregor-Mendel-Institute/nanoPARE
Output files documentation

Hi again Michael. This is comment / enhancement request, not a bug report. I think that new users would benefit from an expanded README or manual that more clearly explains the contents and meaning of ...
  • MikeAxtell
  • Opened 
    on May 2, 2019
  • #4

Gregor-Mendel-Institute/nanoPARE
Python error in endMask.sh

Hi Michael, sorry to spam you with issues (I have a few others to post momentarily), and thanks for responding so fast to the ones from the other day. This pipeline looks like it will be very helpful. ...
bug
  • MikeAxtell
  • Opened 
    on May 2, 2019
  • #3

Gregor-Mendel-Institute/nanoPARE
Unable to run endMap.sh on provided sample data

Trying to test with provided example data, but failing in a way I can t figure out. Successfully ran ./nanoPARE_setup.sh. Then tried to run endMap.sh as follows: ./endMap.sh --cpus 2 --ram 10 -L 1 All ...
  • MikeAxtell
  • 2
  • Opened 
    on Apr 30, 2019
  • #2

Gregor-Mendel-Institute/nanoPARE
gunzip -k option ... -k not universal in all gzip/gunzip installations

endMap.sh decompresses .gz compressed fastq files at line 213 with: gunzip -k -c $fastq_dir/$fastq_file $sample_dir/ $sample_name . $mate_number .fastq https://github.com/Gregor-Mendel-Institute/nanoPARE/blob/05b8f472c694a44ba5d67f061bf2faea873bb32e/endMap.sh#L213 ...
  • MikeAxtell
  • 2
  • Opened 
    on Apr 30, 2019
  • #1
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