Tool for extending reads ?

[medalofhonour]

Hi,

Just wondering if there is any published tool that can extend aligned reads to certain length ? (for ex. extending 100 bp reads to 200 bp). The reads can either be paired-end or single-end.

Any suggestions would be much appreciated.

[Heisman]

I looked into this once and didn't find anything, although there could definitely be something out there. What I ended up doing was getting the bed coordinates from each read, extending them by adding to the flanking region, and then using fastaFromBed from bedtools to grab the extended reads.

[crazyhottommy]

Have a look at HTSeq http://www-huber.embl.de/users/ander...c/tss.html#tss
There is a step to extend the reads to 200bp for ChIP-seq data

[swbarnes2]

I'm not sure why you would want to do this. The reads of your fastq are what's really there. If you are going to supplement them with sequence from a reference, why did you do the experiment in the first place? How will you catch if your sample is different from your reference if you adulterate the experimentally-derived sequences with your reference?