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Old 11-17-2013, 02:39 PM   #1
Location: Brighton

Join Date: Jul 2011
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Default Tool for extending reads ?


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.
medalofhonour is offline   Reply With Quote
Old 11-17-2013, 03:14 PM   #2
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Location: St. Louis

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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.
Heisman is offline   Reply With Quote
Old 11-17-2013, 08:13 PM   #3
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Have a look at HTSeq
There is a step to extend the reads to 200bp for ChIP-seq data
crazyhottommy is offline   Reply With Quote
Old 11-18-2013, 02:41 PM   #4
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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?
swbarnes2 is offline   Reply With Quote

extend reads bam

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