- To generate plots, we use the UCSC bigWigSummary tool to calculate average signal across a feature - for each sample upon request. These values are combined with genotype information extracted from a{" "} + To generate plots, we either use pre-computed, batch-corrected and normalized sample-wise signal matrices, + or use the UCSC bigWigSummary tool to calculate average signal across a feature for each sample + upon request. These values are combined with genotype information extracted from a{" "} Gemini database into a box plot on a server, which is then sent to the user’s browser if they have signed in and agreed to the terms of use. Plots are generated - as needed, rather than in advance, and are derived directly from the count matrix or track and genotype - data. + as needed, rather than in advance, and are derived directly from the matrix or track and genotype data.
- Genome browser tracks were created with the HOMER makeUCSCfile command and{" "}
- bedGraphToBigWig utility from UCSC. Tracks were normalized so that each value represents the read
- count per base pair per 10 million reads. We generate{" "}
+ We generate{" "}
UCSC Genome Browser track hubs upon
- request to visualize averaged track segments for a given genomic feature. These tracks are created on the
- fly by averaging bigWig regions of samples sharing an experimental treatment and genotype, using our
- command-line tool:
+ request to visualize averaged normalized track segments for a given genomic feature. These averaged tracks
+ are created on the fly by averaging bigWig regions of samples sharing an experimental treatment and
+ genotype, using our command-line tool:
bw-merge-window.
- The dark shaded area denotes the distribution of the average RPM values and the light shaded area denotes - the standard deviation. Signals of various epigenetic marks are shown in blue color for non-infected samples - and red color for infected samples. For RNA-seq, forward and reverse transcripts are shown in blue and green - color separately for non-infected samples; while forward and reverse transcripts are shown in red and brown - color separately for infected samples. -
-