The protocol to construct the sequencing library is quite different from the normal TSS mapping promotocol. It is designed to map paired ends reads within a transcript (one on the TSS and the second in the middle of the transcript). To do so, it links them using an adapter with a specific linker for the 5' and 3' ends (TCCAAC and TCCGAC). Sequencing adapters (with barcodes) are then added within the transcript resulting in reads that start on the transcript, goes towards the ends and cover the adapter. This results in the 5' end being sequenced on the reverse, with the TSS located in the middle of the reads. Since we are only interested in the 5' ends, we mapped the adapter to the reads (the reverse-complement of it), extracted the sequence before its starting point (this is the TSS) and get the reverse complement of it. These sequences are then mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).