Description Usage Arguments Examples
Calculates a smoothed track from input count data, and identifies peaks in the data. Outputs the peaks and smoothed track to file.
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bamFile |
Input file in bam format |
bigWigOut |
Produce a smoothed output density file in bigwig format (using wigToBigWig)? |
chromInfo |
UCSC chromInfo.txt file (required only for bigWigOut) |
scratchDirBase |
Directory for scratch output; use local disk for optimal processing. dipPeak writes a significant amount of data to disk as it runs, to reduce memory use. This I/O takes time, and will be faster if you use a local disk or fast mount spot. |
outDir |
Final folder (the files to keep will be moved here from the scratch dir). |
kernel |
'e' for Epanechinov; 'g' for Gaussian; 'm' for Mexican Hat |
cores |
Add additional cores (up to 23) for faster processing. (Default:1) |
perChromCutoff |
Boolean; If yes, calculates a per-chromosome; otherwise, defaults to genome-wide cutoff. |
windowSize |
Choose the size of the smoothing window (default:50) |
windowStep |
Choose the window step (5 will take a window every 5 bases) (default:5) |
indexFile |
Index file made from "samtools index" on the bam input file; deaults to bamFile.bai, or you can provide one. |
retainTemp |
Do you want to retain temporary files? |
limitChrom |
You can limit the smoothing to a list of chromosomes (defaults to everything in the bam file) |
1 | dipPeaks("sequences.bam", bigWigOut="density.bw", outDir="outDir", cores=8);
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