Blog
Performing pathway enrichment with non-human species
Background One of the most popular tools for pathway enrichment analysis for RNA-seq and microarray data is the Gene Set Enrichment Analysis (GSEA) tool by the Broad Institute [1,2]. The database of pathways most often used with GSEA is MSigDB, also by the Broad...
read moreTrimming for RNA-Seq data
Quality trimming decreases the overall number of reads, but increases to the total and proportion of uniquely mapped reads. Thus, you get more useful data for downstream analyses. Too aggressive quality trimming can negatively impact downstream analysis (in our example, estimation of gene expression). Hence, our own findings and that of the research community motivate the incorporation of a light amount of trimming in RNA-seq data (we use a Q threshold of 10).
read moreAn Update From Basepair!
We at Basepair are thrilled to announce some very good news. We have been selected to participate in Entrepreneurs Roundtable Accelerator’s Summer 2017 program for the next four months. This program entails 100,000 dollars of investments, a great working space, and...
read moreBed Bam & Beyond
Among the factors responsible for scaring people away from bioinformatics, the various input and output filetypes surely rank very high. If you want to plot heat maps using ngsplot, you need a bam file. If you want to use deeptools instead, also to make heat maps, you...
read moreTATAA Biocenter partners with Basepair to offer faster NGS data analysis
TATAA Biocenter, the world's foremost organizer of hands-on training in molecular diagnostics and Europe's leading provider of genomic services, has partnered with us, Basepair. We are a leading provider of Next Generation Sequencing (NGS) data analysis solutions, to...
read moreFaster sorting of BAM files: SAMtools vs sambamba
The performance of NGS alignment tools has continuously improved, but sorting the aligned data now takes more time than alignment. A big leap in sorting was recently initiated with SAMtools version 1.x, with support for parallel processing for sorting. We compared the...
read moreBasepair turns 2.0
Basepair was founded in direct response to the challenges I was personally facing with Next Generation Sequencing (NGS) analysis while working at Harvard Medical School and other research institutions. NGS has witnessed a data deluge three times larger than Moore's...
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