cligb: Command line based genome browser for *-seq data

Description

This is currently under development...

• Quick and simple way to visualize a genomic region of your interest accoss many sequence samples
• Query by gene symbol

Requirements

• Python 2.7.5+
• Gviz (Bioconductor package)

Demo

• Clone this repo.

• Downloading a GM12878 (Whole cell/Nucleus) and K562 cell line small RNA-seq data sequenced by ENCODE project from

  • http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/releaseLatest/wgEncodeCshlShortRnaSeqGm12878CellShortAln.bam (53MB)
  • http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/releaseLatest/wgEncodeCshlShortRnaSeqGm12878NucleusShortAln.bam (52MB)
  • http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/releaseLatest/wgEncodeCshlShortRnaSeqK562CellShortAln.bam (46MB)

• Indexing the seq. data is the following command,

  • samtools index bam file
  • move it to PATH_TO_BAM_DIR

• Plotting alignment data in human miR-22:

   $ cligb --help # Show help message
   $ cligb --bam_dir PATH_TO_BAM_DIR/ --symbol hsa-mir-22
  

• Example: hsa-let-7d (Human let-7d)

TODO:

• Packaging for Python command line interface
  • $ cligb --start 1 --end 999 --bams ... --gtf gene.gtf --plot gb.pdf
  • $ cligb --query foxp2 --bams ... --gtf gene.gtf --plot gb.pdf
• Support more query types
• Error handling
• Support to create AnnotationTrack from data is not provided as TxDb.* in Bioconductor packages, for example, miRBase or user-generated GTF/GFF/TSV format.
• More faster and faster to use cache mechanism