Items to add to general run report. - Githubissues

cnobles / iGUIDE

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.

https://iguide.readthedocs.io/en/latest/

GNU General Public License v3.0

20 stars 9 forks source link

Items to add to general run report. #3

Closed cnobles closed 5 years ago

cnobles commented 6 years ago

Consider adding the following to the report:

[completed] karyogram like figure to show genomic distribution of target sites (on/off)
[completed] Compare probable off-target sites against random for enrichment in oncoGenes and specialGenes
[completed] Add Quality control section, showing crossover matrix of probable sites across samples.

cnobles commented 6 years ago

Another point to add:

Given gRNAs with multiple targets, make the report compatible with multi-targeted guides (Table 2 for instance).

cnobles commented 6 years ago

In commit f37cb9bad1cbe43a9e07b38ca1a57176bb8cd03f, added:

genomic density graphic to help with understanding the distribution of incorporation sites and those classified by different bioinformatic criteria (pileups, paired, and matched alignments)
Added enrichment analysis of onco-related genes and special genes testing with fisher's exact.

cnobles commented 6 years ago

Still need to add:

Quality control section
Verify report is compatible with multi-targeted guides

cnobles commented 6 years ago

Multi-targeting guides are now supported. This included adding support to analyze multihits for target sites that had similar flanking sequences. This feature is available in the config file (recoverMultihits) and is TRUE by default. As of version 0.2.1, this feature is available. Most code related to this update is associated with commit 1249ef63b0ae562935eb0cf8f5b7e96eb8c00901.

Still need to add:

Quality control section

cnobles commented 5 years ago

Implemented a runstats report to be generated for each run at the end of processing in v0.9.8 merge (28cc071fb4243c0bf34b3210ae6b6ec00498b8f4). The report offers a quick overview of the read attrition, alignment outcomes, and incorporation breakdown from the run processing. Report output to the reports directory within a project.