Can I use this tools on RNAseq BAM file ?

cancerit / alleleCount

Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)

http://cancerit.github.io/alleleCount/

GNU Affero General Public License v3.0

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Can I use this tools on RNAseq BAM file ? #73

Closed panxiaoguang closed 2 years ago

panxiaoguang commented 2 years ago

I want to calculate the allele-based expression using ASCAT-V3.0 gave loci's file, Dose this tool suit for that?

AndyMenzies commented 2 years ago

We have no experience with ASCAT3.0, we're more familiar with 2.5.X. Assuming the loci file format hasn't changed in the new release, alleleCount should work.

panxiaoguang commented 2 years ago

We have no experience with ASCAT3.0, we're more familiar with 2.5.X. Assuming the loci file format hasn't changed in the new release, alleleCount should work.

Thank you for your quickly reply. I got it