Closed TamaraO closed 6 years ago
Dear Tamara,
I am afraid that this is not that simple. If you want to use it without using our pipeline, you have to make sure that the read names that go into the bam file are integers:
gedi -e FastqFilter -i raw.fastq > reads.fastq
The raw.fastq may also be gzipped or bzipped. Then map reads.fastq with STAR. After that:
gedi -e Bam2CIT -id mapped.cit mapped.bam
gedi -e ResolveAmbiguities -r mapped.cit -g <genomic-index> -s rescued.out -o rescued.cit
The first line creates mapped.cit, the second rescue.out (statistics) and rescued.cit (the mappings to be used in PRICE).
Best, Florian
When are the multi-mapping reads resolved with the RESCUE algorithm? If I run Price using a bam file generated with STAR, will it resolve the multi-mapping reads?
Here are my STAR parameters: