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Removing Adaptors from Next-Gen Data
I had a lot of adapter contamination in a recent ddRADseq Illumina PE HiSeq run and toyed around with a bunch of programs to get rid of it. These two guides in particular were super helpful, so I’m...
View ArticleFour Hundred and Fifty-Four Sequencing
I was reading a great study on hybrid newts when I came across this line: Four hundred and fifty-four sequencing produces additional errors: substitutions and small indels (especially in homopolymer...
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My flexor pollicis brevis hurts
I just finished creating a DNA library for next-generation sequencing, which entails a few days’ worth of pipetting to transport small, precise amounts of liquids between various tubes. I sometimes...
View ArticleConcatenate VCF SNPs into a FASTA Alignment
A while back I published a script, vcf-tab-to-fasta, to make a FASTA alignment from VCF tab files (output from VCFtools‘ vcf-to-tab utility). It just concatenates the SNPs, but it’s useful as a quick...
View ArticleCheap Lab Gear from Amazon.com
After the announcement of Amazon’s tentative plans to deliver items via quadcopters, our lab members joked that it was only a matter of time before you can order restriction enzymes on Amazon and have...
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Goodbye 2013!
Retrospective blog post time, again! 2013 was a fine year. I was lucky enough to go to Bolivia: …and to the Everglades in Florida to see manatees and gators, and to Knoxville, Tennessee for the AAPA...
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