Getting started with TAMA Collapse
TAMA Collapse is a tool used primarily to remove redundant transcript models from long read transcript sequencing read mapping files.
The input for TAMA Collapse is a BAM/SAM file generated by mapping long read transcript sequencing data onto a genome assembly. The BAM/SAM file must be sorted first which can be done using Samtools. You can find a demo SAM file in the TAMA reopository here: test.sam
You will also need the reference genome fasta file that was used for the read mappings. You can find a demo Fasta file in the TAMA reopository here: test_genome.fa
To run TAMA Collapse with default parameters you can use this command:
python tama_collapse.py -s test.sam -f test_genome.fa
Note that in the default setting these parameters are used: -a 10 -m 10 -z 10 -x capped