Bigwigs¶

bincs can create many types of bigwigs for you. A bigwig is a binary file that can be used to visualize your data in genome browsers.

Targets¶

There are several targets to produce bigwigs that display your data in different ways.

In the equations below, C is the total number of ChIP-files while I is the total number of Input-files.

group_merged_chip_vs_merged_input_bigwig¶

This target creates a bigwig for each group, where the pooled ChIP is log2-divided by the pooled Input.

\[log_{2} \frac{RPKM(\sum_{i=1}^{C} {ChIP_i}}{RPKM(\sum_{j=1}^{I} {Input_j})}\]

chip_sample_vs_merged_input_bigwigs¶

This target creates a bigwig of each ChIP-sample log2-divided against the merged input.

\[log_{2} \frac{RPKM_{ChIP_i}}{RPKM(\sum_{j=1}^{I} {Input_j})}\]

The output of this target is {prefix}/data/bigwigcompare/sample_{sample}_vs_merged_input.bw

chip_bigwigs, input_bigwigs¶

These targets create an RPKM-normalized bigwig of each ChIP (or Input) file in your sample sheet.

The output of both these targets are stored in {prefix}/data/bigwig/{sample}.bigwig

merged_chip_bigwigs, merged_input_bigwigs¶

These targets create an RPKM-normalized bigwig of the merged ChIP (or Input) files in your sample sheet.

\[RPKM (\sum_{i=1}^{C} {ChIP_i})\]

or

\[RPKM (\sum_{j=1}^{I} {Input_j})\]

The output of these targets is stored in {prefix}/data/merged_bigwig/{group}_ChIP.bigwig and {prefix}/data/merged_bigwig/{group}_Input.bigwig, respectively.

log2_ratio_group_vs_group_bigwig¶

This target creates a log2-ratio bigwig for each combination input-normalized group against each other. It requires more than one group in your sample sheet.

C1 and C2 is the total number of ChIP-files in group 1 and 2, respectively. I1 and I2 is the same for input.

\[log_{2} \frac{log_{2} \frac{RPKM(\sum_{i=1}^{C1} {ChIP Group1_i})}{RPKM(\sum_{j=1}^{I1} {Input Group1_j})}} {log_{2} \frac{RPKM(\sum_{k=1}^{C2} {ChIP Group2_k})}{RPKM(\sum_{l=1}^{I2} {Input Group2_l})}}\]

The output of this target is stored in {prefix}/data/bigwigcompare/group_{group1}_vs_group_{group2}.bigwig