Bam

Downsampling bam files to a certain number of reads

When compare different ChIP-seq data sets or analyze a set of ChIP-seq data sets together (e.g. ChromHMM analysis), it is desirable to subsample the deeply…

convert bam to fastq and remap it with bwa mem

Sometimes, you get a processed bam file from other resources, but you want to map it with another aligner. For example, the old BWA aln does not keep the…

convert bam file to bigwig file and visualize in UCSC genome browser in a Box (GBiB)

I just came across UCSC genome browser in a box Gbib, and I want to try it out.

rehead a bam file

I downloaded some ChIP-seq bam files from the UCSC genome browser

count how many mapped reads in a bam file

I wanted to count how many mapped reads are in a ChIP-seq bam file downloaded from UCSC ECODE project.

convert Eland sorted.txt to bam file

I downloaded a human ChIP-seq data set mapped to hg18 from NCBI GEO.