When it comes to finding/using established tools I am completely untrained.
We are starting with illumina paired-end reads (we don't necessarily care if the analysis is done with tools supporting paired-ends per se, the sequencing just happened to be done this way). The paired ends have already been separated by the sequencer pipeline.
In an earlier post I asked how one would trim for quality, and I found a few tools to do that.
Now I'm supposed to perform an alignment and use the alignment information to get expression profiles. (Eventually we would like to use these expression profiles to compare different samples.)
It seems like cufflinks should be able to do this sort of thing (I'm assuming it would be working in partnership with bowtie or tophat for this.). Are there any other pipelines and how would I best find the sequence of commands that would prepare the data and produce the mapping files that I need to run these analyses?
We are starting with illumina paired-end reads (we don't necessarily care if the analysis is done with tools supporting paired-ends per se, the sequencing just happened to be done this way). The paired ends have already been separated by the sequencer pipeline.
In an earlier post I asked how one would trim for quality, and I found a few tools to do that.
Now I'm supposed to perform an alignment and use the alignment information to get expression profiles. (Eventually we would like to use these expression profiles to compare different samples.)
It seems like cufflinks should be able to do this sort of thing (I'm assuming it would be working in partnership with bowtie or tophat for this.). Are there any other pipelines and how would I best find the sequence of commands that would prepare the data and produce the mapping files that I need to run these analyses?
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