Monthly Archives: July 2014

Error with HTSeq

Posted on July 15, 2014 by Lisa Johnson

Running HTSeq to get raw read counts associated with chromosomal positions/annotated genes from sorted .bam files: Error occurred when processing SAM input (record #30675291 in file {PATH}/tophat/Exp-1-Basal/accepted_hits.sorted.bam): Maximum alignment buffer size exceeded while pairing SAM alignments. [Exception type: ValueError, raised … Continue reading →

Posted in Bioinformatics, software | Leave a comment

gene set enrichment analysis (GSEA)

Posted on July 10, 2014 by Lisa Johnson

What is a gene set enrichment analysis? What is a reasonable enrichment score? With the genes in common between the two groups from yesterday’s venn diagram, I want to see what functions they correspond to. There are many ways to assign functions … Continue reading →

Posted in Bioinformatics, Data Analyses | Leave a comment

Venn Diagrams

Posted on July 9, 2014 by Lisa Johnson

Today’s adventures in Venn Diagrams. Seems like a simple task, right? Two (or more) circles with numbers in the middle. I want to use this visualization graphic to show the number of genes differentially expressed between 2 sets of groups. … Continue reading →

Posted in Bioconductor, Bioinformatics, R | Leave a comment