Missing files

[staciawyman]

Hello, There are several files missing from the distro for LongAmp such as longamp_delly_calling.sh and longampfigures_distribution.py. Is there a reason these were left out?

Also is there some reason for using hg19 instead of the current version of the genome? Thank you.

[mcao0404]

Thanks for your questions. We have iterated this pipeline but seems some texts were not corrected updated.

We don't use Delly for variant calling so removed lthe ongamp_delly_calling.sh script. And we rewrite the longampfigures_distribution.py to a new file called distribution_LAS.py. Further correction w/ repo description will be updated later (ASAP).

We used hg19 as we started our research years ago and have better annotation w/ hg19. You could use your own reference instead.

Let me know if you have further questions.

Best, Ming

[staciawyman]

Got it. Thanks for the prompt response!

[staciawyman]

The REAME says to use longamp_bwa_PCR.sh, but that script calls delly. Was delly used for the paper "Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing"?

# delly variant calling
  # update 11/11/2020
  bash longamp_delly_calling.sh ${ref_genome}

[mcao0404]

The REAME says to use longamp_bwa_PCR.sh, but that script calls delly. Was delly used for the paper "Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing"?

# delly variant calling
  # update 11/11/2020
  bash longamp_delly_calling.sh ${ref_genome}

That's from longamp_bwa_cellline.sh not longamp_bwa_PCR.sh, please use longamp_bwa_PCR.sh. We didn't use delly in the main context of that paper.