Copy number analysis using 454 data

[ps376]

Hi,

I am pretty new to sequence analysis in general, but I was wondering if anyone know how to identify amplifications and deletions from 454 sequencing data? Intuitively, I would feel the coverage or read depth would indicate read depth (not sure about amplifications). But I'm not sure if this is the best way to go about it. Does anyone have any experience with this?

Thanks!

[gprakhar]

Hello,

There are multiple tools available to detect CNV's.
Please take a look at these previous threads.
http://seqanswers.com/forums/showthread.php?t=11871
http://seqanswers.com/forums/showthread.php?t=9480

They may refer to detecting CNV in Exome Capture data, but the programs can be used for WGS data too.

Regards,
--
pg

[henry.wood]

It may be too late for you to make this choice, but the 454 isn't really the best platform to be doing CNV work. Its strength is the length of the read, but to detect CNVs using read depth, the number of reads is the most important. As long as you have enough bases to align the read to the genome then that is enough.
If you have already got data, then yes, it is possible. There are loads of tools on the wiki that can do the job. Some of them might sulk at the low number of reads you get from 454 data.

[ps376]

CNVer

Hi,

Thanks for the replies! I found CNVer on the wiki. They claim to work with low-depth targeted sequencing kind of data (454) and use paired end information rather than depth of coverage.

Anyone used this?