Milos Pjanic's repositories
sam2BigWig
Convert SAM files to BIGWIG files. This script will take a sam file mapped to the human genome hg19 and convert it to a bigwig file for UCSC Genome Browser. Dependencies samtools, bedtools bamtobed, downloads/executes bedItemOverlapCount, bedGraphToBigWig and fetchChromSizes.
bamsplit2bigwig
Convert bam file mapped to the human genome hg19 to two strand specific bigwig files for UCSC Genome Browser. Useful to visualize nucleosomal or protein binding ChIP-Seq 'footprints' marked by reads mapping on different DNA strands. Bamsplit2bigwig depends on bedtools bamtobed, bedItemOverlapCount, bedGraphToBigWig and fetchChromSizes.
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tabsep
Formatting of multiple spaces and tabs to a single tab, useful for for quick table formatting.
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