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Laurence Ettwiller edited this page Jun 22, 2015 · 8 revisions

Welcome to the TSS wiki

The website for the project is here.

**The pipeline to call TSS at one base resolution is the following : **

    1. Quality and adaptor trimming of the reads
    1. Mapping the reads to the reference genome : RECOMMENDED FOR 1 BASE RESOLUTION : Bowtie2 --local
    1. bam2firstbasegtf.pl --bam control.bam --cutoff 0 > control.gtf
    1. bam2firstbasegtf.pl --bam cappable.bam --cutoff 1.5 > cappable.gtf
    1. filter_tss.pl --tss cappable.gtf --control control.gtf --cutoff 0 > TSS_enriched.gtf
    1. cluster_tss.pl --tss TSS_enriched.gtf --cutoff 5 > TSS_enriched_cluster_5.gtf

If you do not have a control, you can skip the filtering step :

    1. Quality and adaptor trimming of the reads
    1. Mapping the reads to the reference genome : RECOMMENDED FOR 1 BASE RESOLUTION : Bowtie2 --local
    1. bam2firstbasegtf.pl --bam cappable.bam --cutoff 1.5 > cappable.gtf
    1. cluster_tss.pl --tss cappable.gtf --cutoff 5 > cappable_cluster_5.gtf
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