Cross-mappability from gene A to gene B, crossmap(A,B), is defined as the number of gene A's k-mers (75-mers from exons and 36-mers from UTRs) whose alignment start within exonic or untranslated regions of gene B. Cross-mappability has been described in the following paper.
Saha A, Battle A. 2018. False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment error.
- These check pre-requisites before computing cross-mappabilities from the prerequisites page.
- Compute cross-mappabilites genome-wide following instructions step by step from this page.
You may download already computed cross-mappability resources for human genome (hg19 and GRCh38) from here.
Saha A, Battle A. 2018. False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment error.
Ashis Saha ([email protected])