Removal of poor quality reads before alignment

[gibsongenetics]

Hello,

So I have recently recieved a whole slide worth of Paired-End SOLID ChIP-seq data, and have encountered problems at the earliest of steps. I have tried to use BOWTIE to align these reads to the hg19 genome, but it is going extremely slow. Upon further inspection it seems that there are a number of reads with "no-calls" or otherwise poor quality values that may or may not be "gumming up" the Bowtie aligner... the question:

Does anyone have suggestions on how to pre-process the data to remove reads that are VERY unlikely to give unique alignments prior to mapping to a reference genome? I'm thinking like... anything with average quality values below 8 gets thrown out...

Any help in how to do this, or aligners that may do this or something similar would be great.

Many thanks,
Bryan

[gibsongenetics]

I guess I should qualify this by saying, does anyone know if there is a way to pre-process the paired files without losing pairing info that aligners like BOWTIE and such would use? I don't think the fastx / galaxy is capable of this, right?

[kmkocot]

Hi Bryan,

You might check out lucy:

http://lucy.sourceforge.net/

seqclean:

http://compbio.dfci.harvard.edu/tgi/software/

and RepeatMasker:

http://www.repeatmasker.org/

I hope these are helpful.

Kevin