Psst! I've posted some details about my notebook setup here.

How to distinguish perfectly mapped reads from a SAM/BAM file

In which I explore read alignments in SAM format and discuss the pros and cons of various approaches to distinguishing perfect matches from imperfect matches.

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Summary table for iLocus paper

I created a table for my iLocus paper tonight, and wanted to capture the commands used to populate it while everything is still fresh in my mind.

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Is RefSeq's Arabidopsis annotation TAIR10?

Some notes on my data forensics to determine whether there are any differences between the RefSeq Arabidopsis annotation and TAIR10.

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Cleanup: supplementary tables for our genome paper

We submitted a genome paper to Genome Biology over the weekend. I'm going through our repository and tidying things up, and I realized I have not had a chance to record my notes on several of the supplemental tables providing a comparison of genome features across seven species. I'll go ahead and do so here.

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