Hello all.

 

I have short read sequences for RNASeq that I have then aligned to the reference transcript sequences.  The reads are from a Solexa platform and they were aligned using MAQ.  I have imported the data using ShortReads (readAligned) and all looks good.  However, I am interested in limiting the data to those transcripts with at least 85% coverage.  I can’t find any documentation to do this that doesn’t involved looking at each transcript individually.  Any way to do this for all transcripts (30,000+)? 

 

Also, while I am writing, I was interested in only looking at reads above a certain quality score.  When I input the data with readAligned, I couldn’t figure out how to filter on this variable, so I ended up reading the data just into R, filtering that way, and then reading the data into ShortRead.  Is there a better way to do this?  All the transferring of the data back and forth took a lot of time to process.

 

Lastly, any good online resources for RNASeq applications with Bioconductor that people can recommend?  

 

Thank you,

 

Jessica


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