BAM Conversion to Other Formats

genomeCoverageBed ^*

Authors

Menachem Sklarz

Affiliation

Bioinformatics core facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

A module for running bedtools genomecov:

The module builds a bedgraph (bdg) file based on an existing BAM file.

Requires

• BAM file in the following slot:

  • sample_data[<sample>]["bam"]

Output

• Puts output BedGraph files in the following slots:

  • sample_data[<sample>]["bdg"]

Parameters that can be set

Parameter	Values	Comments
-g	path to chrom.sizes	You must redirect the -g parameter. Create the chrom.sizes file for the reference genome with samtools faidx followed by cut -f1,2.

Lines for parameter file

genCovBed_bwt1:
    module: genomeCoverageBed
    base: sam_bwt1
    script_path: /path/to/bedtools/bin/genomeCoverageBed
    redirects:
        -bg: 
        -g: /path/to/ref_genome/ref_genome.chrom.sizes

References

UCSC_BW_wig

Authors

Menachem Sklarz

Affiliation

Bioinformatics core facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

A module for creating wig and bigwig files using UCSC tools:

The module creates bigwig and wig files from the current active BedGraph file.

Requires

• BedGraph file in the following slot:

  • sample_data[<sample>]["bdg"]

Output

• Puts output sam files in the following slots:

  • self.sample_data[<sample>][“bw”]

  • self.sample_data[<sample>][“wig”]

Parameters that can be set

Parameter	Values	Comments
bedGraphToBigWig_params	e.g. -blockSize=10 -itemsPerSlot=20	Parameters to pass to bedGraphToBigWig
bigWigToWig_params	e.g. -chrom X1 -start X2 -end X3	Parameters to pass to bigWigToWig
script_path		Path to dir where UCSC tools are located.
scope	sample|project	Where the ‘bdg’ is located

Note

Set script_path to the path of the UCSC tools, not to a specific tool!!! If they are in the PATH, as when installing with CONDA, leave the script_path empty. Both bedGraphToBigWig and bigWigToWig will be executed. To set specific params, use bedGraphToBigWig_params and bigWigToWig_params, respectively.

Lines for parameter file

UCSCmap_bams:
    module:         UCSC_BW_wig
    base:           genCovBed_sam
    script_path:    /path/to/ucscTools/kentUtils/bin/
    genome:        /path/to/ref_genome.chrom.sizes
    bedGraphToBigWig_params:     -blockSize=10 -itemsPerSlot=20
    bigWigToWig_params:          -chrom X1 -start X2 -end X3

References

Kent, W.J., Zweig, A.S., Barber, G., Hinrichs, A.S. and Karolchik, D., 2010. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics, 26(17), pp.2204-2207.

IGV_count ^*

Authors

Menachem Sklarz

Affiliation

Bioinformatics core facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

A module for running IGVtools count:

Requires

• Either SAM or BAM files in the following slots:

  • sample_data[<sample>]["bam"]

  • sample_data[<sample>]["sam"]

Output

• Puts output tdf or wig files in one the following slots:

  • self.sample_data[<sample>]["wig"]

  • self.sample_data[<sample>]["tdf"]

Parameters that can be set

Parameter	Values	Comments
format	wig|tdf	Determines whether to create a ‘wig’ or ‘tdf’ file.
genome		Path to chrom.sizes file for reference genome

Lines for parameter file

IGVcount1:
    module: IGV_count
    base: samtools1
    script_path: java -Xmx1500m -jar /path/to/igvtools.jar count
    format: tdf   # Options: 'tdf' or 'wig'
    genome: /path/to/genome.chrom.sizes

References

Thorvaldsdóttir, H., Robinson, J.T. and Mesirov, J.P., 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in bioinformatics, 14(2), pp.178-192.

IGV_toTDF ^*

Authors

Menachem Sklarz

Affiliation

Bioinformatics core facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

A module for running IGVtools toIGV:

Requires

• WIG file in the following slot:

  • sample_data[<sample>]["wig"]

Output

• Puts output tdf file in one the following slots:

  • self.sample_data[<sample>]["tdf"]

Parameters that can be set

Parameter	Values	Comments
genome		Path to chrom.sizes file for reference genome

Lines for parameter file

IGV2TDF:
    module: IGV_toTDF
    base: samtools1
    script_path: /path/to/bin/java -Xmx1500m -jar /path/to/igvtools.jar toTDF 
    genome: /path/to/genome.chrom.sizes

References

Thorvaldsdóttir, H., Robinson, J.T. and Mesirov, J.P., 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in bioinformatics, 14(2), pp.178-192.