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How to compare two BAM files using deeptools?
This tool compares two BAM files based on the number of mapped reads. To compare the BAM files, the genome is partitioned into bins of equal size, then the number of reads found in each bin is counted per file, and finally a summary value is reported.
How is bamcoverage used in deeptools2 NGS analysis?
The bamCoverage command (part of the deeptools2 package) allows you to convert alignment files (in BAM format) to other alignment formats. This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.
Which is the correct format for bamcompare 1?
The format is scaleFactor1:scaleFactor2.For example, –scaleFactor 0.7:1 will cause the first BAM file tobe multiplied by 0.7, while not scaling the second BAM file (multiplication with 1). Possible choices: log2, ratio, subtract, add, mean, reciprocal_ratio, first, second The default is to output the log2 ratio of the two samples.
When to use the reciprocal ratio in bamcompare?
The reciprocal ratio returns the the negative of the inverse of the ratio if the ratio is less than 0. The resulting values are interpreted as negative fold changes. Instead of performing a computation using both files, the scaled signal can alternatively be output for the first or second file using the ‘–operation first’ or ‘–operation second’.
How is the scaled signal output in deeptools?
Instead of performing a computation using both files, the scaled signal can alternatively be output for the first or second file using the ‘–operation first’ or ‘–operation second’. (Default: “log2”) A small number to avoid x/0. Only useful together with –operation log2 or –operation ratio.
Which is an example of a module in deeptools?
The deepTools modules bamCompare and bamCoverage not only allow for simple conversion of BAM to bigWig (or bedGraph for that matter), but also for normalization, such that different samples can be compared despite differences in their sequencing depth.
How is deeptools used in ChIP seq analysis?
To get a feeling for what deepTools can do, we’d like to give you a brief glimpse into how we typically use deepTools for ChIP-seq analyses. For more detailed exampes and descriptions of the tools, simply follow the respective links.