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Old 11-17-2013, 02:39 PM   #1
medalofhonour
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Default Tool for extending reads ?

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.
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Old 11-17-2013, 03:14 PM   #2
Heisman
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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.
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Old 11-17-2013, 08:13 PM   #3
crazyhottommy
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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
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Old 11-18-2013, 02:41 PM   #4
swbarnes2
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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?
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