CC set up and performed the majority of the bioinformatics on the sequencing runs including data retrieval, read alignments, differential gene expression analysis, KEGG pathway analysis, data interpretation and co-wrote the main manuscript with MSM.
Despite that, a progressiveMauve alignment with differential content can be trivially reduced to contain only segments conserved among all taxa of interest, yielding a signed gene-order permutation matrix that is suitable for current genome rearrangement inference software.
One factor that could contribute to asymmetrical alignment is differential affinity between each clone's TCR and cognate antigen.
The typical tasks include analysis of RNA-seq data (QC, preprocessing, alignment, quantitation, differential expression analysis, filtering and pathway analysis), ChIP-seq data (QC, preprocessing, alignment, peak calling, filtering, motif discovery and pathway analysis) and exome/genome-seq data (QC, preprocessing, alignment, variant calling and filtering).
In one set of sequence alignments a differential IES retention/excision event between paralogous regions was jointly detected for two species (supplementary fig. S2, Supplementary Material online).
Two stand-alone applications developed with HTSeq are distributed with the package, namely htseq-qa for read quality assessment and htseq-count for preprocessing RNA-Seq alignments for differential expression calling.
Rather than excluding such probes, we noted that there was a continuum of differential alignment biases, so we took an empirical approach.
In Additional file 1: Figure S3, to test the influence of the input parameters to both Tophat and Cuffdiff the workflow was redone changing one parameter of the alignment (Tophat) or differential expression (Cuffdiff) analysis.
Compared to static culture, pulsatile flow increased seeded ASMC growth by 70%, improved the homogeneity of cell distribution within the TDCCs and induced differential cellular alignment depending on the primary stimuli.
