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Old 05-15-2011, 02:12 PM   #1
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Location: ny

Join Date: Aug 2010
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Default Removal of poor quality reads before alignment


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,
gibsongenetics is offline   Reply With Quote
Old 05-15-2011, 03:40 PM   #2
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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?
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Old 05-16-2011, 05:22 AM   #3
Location: Alabama

Join Date: Jun 2009
Posts: 48

Hi Bryan,

You might check out lucy:


and RepeatMasker:

I hope these are helpful.

kmkocot is offline   Reply With Quote

alignment, bad reads

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