Category: BINF 6203

Sidebar: DE with Tuxedo pipeline #usegalaxy

Sidebar: DE with Tuxedo pipeline #usegalaxy

To get around the problems with the software installs in the lab (and that some of you are having installing corset on your own) here is another way to get a full DE gene...

BINF 6203: Lab 10 — expression statistics

BINF 6203: Lab 10 — expression statistics

Last week you used transcriptome and read mapping tools to get read counts for your Vibrio vulnificus expression data, with two different pipelines. Now let’s analyze the data and get the top differentially expressed...

BINF 6203: Lab 9 — RNA-Seq read summarization

BINF 6203: Lab 9 — RNA-Seq read summarization

In this lab and the next, we are going to use two different methods to calculate differential expression for the same RNASeq dataset. In a nutshell, we have measured gene expression under two conditions...

BINF 6203: Genomics

BINF 6203: Genomics

This is the game plan for BINF 6203 — Genomics in Spring Semester 2015. Class times: 11:00-12:15 MW Lab: 12:15-2:00 M Links to these posts will also be provided in Moodle, but this post...

BINF 6203: Lab 8 — Simple variant calling

BINF 6203: Lab 8 — Simple variant calling

This lab takes us back to the tomato chloroplast genome data again. You’ve QCed the chloroplast data in Lab 2, assembled it in Lab 3, produced a consensus sequence from mapped reads in Lab...

BINF 6203: Lab 7 — Genome comparison with Mauve

BINF 6203: Lab 7 — Genome comparison with Mauve

As we started on comparative genomics, we covered three main concepts. First, how do you decide which genes are “the same” across multiple genomes, i.e. orthologs, genes having a common ancestor and related by...

BINF 6203: Lab 6 — Browsers and tracks

BINF 6203: Lab 6 — Browsers and tracks

You can think of genomic data formats in a few main categories: Sequence data (FASTA, FASTQ) Alignments (BLAST results, SAM and BAM files) Track data (genomic intervals, WIG files — continuous value tracks) Tabular data...

BINF 6203 — Lab 5: Generating annotation for a genome

BINF 6203 — Lab 5: Generating annotation for a genome

In this lab exercise, you’ll use the myRAST software to annotate an E. coli genome assembly that you generated a couple of weeks ago. We requested that myRAST be installed on the lab computers,...

BINF 6203 — Lab 4: Read mapping

BINF 6203 — Lab 4: Read mapping

Mapping short sequence reads to a reference sequence is a common task in genomics. Many different results can be extracted from a mapped sequence, depending on the original experimental design that produced the sequence...