Versions Compared

Old Version 2

changes.mady.by.user Deatherage, Daniel E

Saved on

compared with

New Version Current

changes.mady.by.user Deatherage, Daniel E

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Note
titleThe remaining portion of this tutorial requires the runs to have completed
Code Block
languagebash
titleYou can also check how many have finished with this command
cd $SCRATCH/GVA_breseq_multi-sample
tail -n 1 logs/*|grep -c "+++   SUCCESSFULLY COMPLETED"

Until the above returns 7 the following commands will not work correctly.

While you wait consider going back to the intro breseq tutorial to rerun the sample that you took through read QC, mapping, SNV calling, and visualization. or skip to the bottom of the page for other potentually useful tutorials.

Grouping .gd files together

...

Data analysis with breseq (like all other programs) is only as good as the data that goes into it. The MultiQC and Trimmomatic tutorials work well upstream of breseq, while the identification of novel DNA elements may be useful for things such as trying to identify unknown plasmids and makes use of the genome assembly tutorial.

Alternatively, again consider going back to the intro breseq tutorial to rerun the sample that you took through read QC, mapping, SNV calling, and visualization.



Back to the GVA2020 page