removing adapters sequences from ChIPseq data?

johannes.rainer · 02-05-2010, 07:50 AM

dear all,

I've just got raw sequencing reads for a ChIPseq experiment and right now I want to filter the data prior to aligning the reads to the genome. here are now my quations:
1) do i need to filter the data for PCR primers and adapters?

2) if yes, should i expect the adapters to be sequenced only on the 3' end of the sequenced reads? in other words, should i trim adaptor sequences only from the right of the reads (e.g. using the trimLRPatterns function from Bioconductor's ShortRead package)

3) what about the primer sequences?

4) should i expect reverse complements of primers/adapters in the reads?

5) is there some sort of "gold-standard" how sequencing data should be preprocessed before being aligned to the genome?

sorry for all these questions, but I'm fairly new to the whole filed...

thanks for your answers!

cheers, jo

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02-05-2010, 07:50 AM	#1
johannes.rainer Junior Member Location: Innsbruck, Austria Join Date: Feb 2010 Posts: 1	removing adapters sequences from ChIPseq data? dear all, I've just got raw sequencing reads for a ChIPseq experiment and right now I want to filter the data prior to aligning the reads to the genome. here are now my quations: 1) do i need to filter the data for PCR primers and adapters? 2) if yes, should i expect the adapters to be sequenced only on the 3' end of the sequenced reads? in other words, should i trim adaptor sequences only from the right of the reads (e.g. using the trimLRPatterns function from Bioconductor's ShortRead package) 3) what about the primer sequences? 4) should i expect reverse complements of primers/adapters in the reads? 5) is there some sort of "gold-standard" how sequencing data should be preprocessed before being aligned to the genome? sorry for all these questions, but I'm fairly new to the whole filed... thanks for your answers! cheers, jo