Somatic APP analysis download

Implemented code for the reanalysis of somatic APP retrotransposition originally claimed by Lee at el (Nature, 2018). Modules for two different analyses--detection of intra-exonic junctions (IEJs) and estimation of APP gencDNA fraction--are provided. A detailed description of our analysis is available in our bioRxiv paper (https://bit.ly/35Kgfbu).

[ Basic usage ]
• Detection of IEJs connecting APP exons
java -jar somaticAPP.jar -D -b input.bam [optional_arguments]
* Input data: PRJNA577966
* The input bam should be mapped to APP751.fa (provided in the 'data' folder) and sorted by read name after mapping

• Estimation of gencDNA fraction
java -jar somaticAPP.jar -F -b input.bam -a BWA_PATH -s SAMTOOLS_PATH [optional_arguments]
* Input data: PRJNA493258
* The input bam should be a human-genome-mapped (hg38), coordinate-sorted, and duplicate-marked file.

Try -h or -? options to get detailed descriptions for optional input parameters

Project Activity

See All Activity >

Follow Somatic APP analysis

Somatic APP analysis Web Site

Other Useful Business Software

Sales CRM and Pipeline Management Software | Pipedrive

The easy and effective CRM for closing deals

Pipedrive’s simple interface empowers salespeople to streamline workflows and unite sales tasks in one workspace. Unlock instant sales insights with Pipedrive’s visual sales pipeline and fine-tune your strategy with robust reporting features and a personalized AI Sales Assistant.

Try it for free

Rate This Project