SNP calling with RNA seq

[Homa]

Hello,

I have RNA-seq data sequenced in Illumina platform.

I have run the quality control with FASTQC and indeed, I have detected duplicates. As I am going to use these sequence data to do the SNP calling, I must remove the duplicates.

Does anyone have any experience with this? what is the best way to remove the duplicates, before mapping or when I start with the SNP calling with gatk?

Also, what are the software suggested for this purpose.

Thanks a lot in advance.

PS: I have posted this question to www.biostars.org/p/66831/, the answers are not consensus.

[jgibbons1]

I use the fastx_collapster to remove duplicates.

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_collapser_usage

If you get a buggy error message about quality scores plug the -Q33 argument into the command line.

[Krish_143]

I am using filterPCRdupl.pl.
source:

http://code.google.com/p/condetri/downloads/detail?name=filterPCRdupl.pl

[mbayer]

Hi Homa,

duplicates are a fact of life with RNASeq. In fact, we regularly see 80-90% duplication in our RNASeq here. I always remove duplicates before SNP calling as it reduces the false positive rate, and I use samtools rmdup to do this after I have mapped the reads for each sample, then I merge the samples. I also retain the undeduped files -- this is useful in case you want to do quantitative analysis (for which you do not want to remove duplicates!).

cheers
Micha