I want to follow the following method to analysis replication timing. I am wondering could I finish all these analysis in Galaxy project website and which tools I should use to do it?
" 1. Map sequencing data to the corresponding genome using bowtie2 or any reliable short read aligner. Define varying-size, equal-coverage chromosomal windows as segments covered by 200 reads in the G1 fraction and count S phase reads in the same windows. 2. Calculate the S/G1 ratio for each window. This should generate a map with large fluctuations in the S/G1 ratio along the genome (Figure 3). A good control for the reliability of the ToR measurements is to compare this map to the G1/G1 ratio (from two separate measurements of G1) which should be much flatter. 3. Normalize data to 0 mean and 1 SD by subtracting from each value the average value of all windows (excluding the X chromosome) and dividing the results by the standard deviation of the S/G1 of all windows. This is done in order to convert to z scores and enable comparison between different experiments. 4. Remove all gap regions listed by the UCSC genome browser as well as each remaining inter gap fragment containing fewer than 15 data windows. −16 5. Smooth the remaining fragments with a cubic smoothing spline via the Matlab function csaps with a parameter of 10 and interpolate at set points every 100 kb. NOTE: Parameters of smoothing and interpolation should be adjusted based on the depth of the data. Other suitable smoothing methods and functions exist and can be used. 6. After visually confirming the reliability of each replicate, merge all the reads and calculate a deeper resolution profile by performing the same process described above on this data. "
Thanks,
Weiyan
This looks taken from a paper. It might help if you provide a link to this paper.