Posts Categorized: Workflows

Sifting Sands

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Below is a quick workflow I am using to help Drinan annotate ~1.5 million sequences from an amplicon targeting NGS effort of sand. head /Users/sr320/Dropbox/hummingbird-ipython-nbs/data/DanD/meiofauna_forward_sequences.fa >M02215:33:000000000-AFA9E:1:1101:14961:2005 1:N:0:15 TGACTGTGCTAAGGTAGCATAATTAATTGTCTTTTAATTAGAGACTTGTTTGAAAGATTT TTTGAATTTAATATAGTTTTAAAATTATAAAAATGAATTTTTATATATTGGTAAAAATAC CATGATTTTTTAAAAAGACGATAAGACCCTATCAAGTTTTACTTAAATTTAAAGAAAATT TAGGTTTTAATGGGGCATTATTATTTATTTTAAATAAATTTTGATCTTAAATTAAATTTT AGGAAATTTAATAAAATTACTGTAGGGATAACAGTGTAATATTTTTTAAAGTTCATATTT A >M02215:33:000000000-AFA9E:1:1101:11050:2011 1:N:0:15 TAACTGTGCTAAGGTAGCATAATCACTTGTCTCCTAATTAGAGACTGGCATGAAAGGGTA AACTCTTTATAACTTTATAAAGCATACACACTGAAATTTTTATTTAGACGAAGAAATCTA       Within a given working directory I proceeded to (in Jupyter NB) cp meiofauna_forward_sequences.fa query.fasta –… Read more »

Developing CpG O/E Workflow

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In an effort to streamline CpG O/E determination across various transcriptomes, here is my latest attempt. tldr; Ahyacinthus = This is dependent on have GO slim annotations for all genes – for this particular case the annotation pipeline can be seen here.      

RNA-Seq: Tophat via iPlant

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Goal: Use RNA-seq to compare expression between oysters (n=3) pre and post heat shock. Based on IPlant Collaborative Tutorial https://pods.iplantcollaborative.org/wiki/display/eot/RNA-Seq_tutorial Task 1: Align read data to Crassostrea gigas genome. Tophat is a specialized alignment software for RNA-seq reads that is aware of splice junctions when aligning to a reference assembly. 1) Click Apps from DE… Read more »