How to get spanning reads which support the fusion event?

[qianlanyao]

Where can I find the detail sequences of spaning or split reads which supported the breakpoint in the output results? For example, like the figure 6f and 6g in your article.

[Andrew]

There is a previously undocumented script get_reads.pl that can be used for this purpose. I have added a small description of how to use the script to the defuse 0.6.1 manual page.

[qianlanyao]

Thank you. But how can i get the original sequence of spanning support reads using defuse 0.6.0?

[Andrew]

To obtain the original sequence for spanning reads, search the reads.1.fastq file and reads.2.fastq file in the output directory for the fastq entry with the associated read id. The read id is the first column in the spanning read list.

Alternatively, use something like the attached script which makes use of an ad-hoc index that is created by defuse for the fastqs.