Hi

I am analyzing deep sequencing data and I would like to manipulate these large data  (>100,000 reads - can be either fasta or bam format) to do the followings:

#1 - Exclude primer sequences (short strings of 25-30 nt) 

e.g. if I want to exclude all the match 'CAAACTCAAATCTAATCTAACCAAAAAAAC' and 'CAACCTTTTAATCTAACCAAAAAAAC'  

#2 - Filter out the short reads (< a 100 bp)?

#3 - And finally exclude reverse oriented sequences?

I am using outside R tools (samtools) but it would be great to have all running in R...

thanks in advance!

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