Efficiently analyze the density of short DNA sequence read alignments in the BAM file format.
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Read counts across one or more BAM files are grouped, normalized, summarized, and graphed in interactive html files. The code is efficient and multithreaded, e.g. a 1.7 GB BAM file can be processed in under 10 seconds.
See these interactive graphs showing example bamliquidator output:
A BAM file is a binary sequence alignment map -- see SAMtools for more info: http://samtools.sourceforge.net/
The full bam file can be analyzed, or specific regions can be analyzed via .gff or .bed files.
The read counts and summaries are stored in HDF5 format where they can be efficiently read via Python PyTables or the HDF5 C apis. The HDF5 files can be viewed directly with the cross platform tool HDFView. There is an option to output the data in tab delimited text files as well.
There is also a command line utility for counting the number of reads in specified portion of a chromosome, and the count is output to the console.
For more info, please see https://github.com/BradnerLab/pipeline/wiki/bamliquidator
Source code is available under the The MIT License (MIT) at https://github.com/BradnerLab/pipeline , e.g. see https://github.com/BradnerLab/pipeline/tree/master/bamliquidator_internal/Dockerfile . Bamliquidator makes heavy use of samtools, which is also distributed under the MIT licence -- see https://github.com/samtools/samtools for more details.
$ wget https://www.dropbox.com/s/a71ngagu2k8pgiv/04032013_D1L57ACXX_4.TTAGGC.hg18.bwt.sorted.bam.bai
$ wget https://www.dropbox.com/s/bu75ojqr2ibkf57/04032013_D1L57ACXX_4.TTAGGC.hg18.bwt.sorted.bam
$ mkdir output
$ time docker run --rm --user `id -u`:`id -g` \
-v $PWD:/input:ro -v $PWD/output:/output \
--pull=always \
bioliquidator/bamliquidator \
/input/04032013_D1L57ACXX_4.TTAGGC.hg18.bwt.sorted.bam -o /output
Liquidating /input/04032013_D1L57ACXX_4.TTAGGC.hg18.bwt.sorted.bam (file 1 of 1)
Liquidation completed: 5.242445 seconds, 29059326 reads, 5.531770 millions of reads per second
Cell Types: input
Normalizing and calculating percentiles for cell type input
Indexing normalized counts
Plotting
-- skipping plotting chrM because not enough bins (only 1)
-- skipping plotting chrM because not enough bins (only 1)
Summarizing
Post liquidation processing took 2.068062 seconds
real 0m9.044s
user 0m0.108s
sys 0m0.012s
$ ls output
chr10.html chr12.html chr14.html chr16.html chr18.html chr1.html chr21.html chr2.html chr4.html chr6.html chr8.html chrX.html counts.h5 summary.html
chr11.html chr13.html chr15.html chr17.html chr19.html chr20.html chr22.html chr3.html chr5.html chr7.html chr9.html chrY.html log.txt
Content type
Image
Digest
Size
138.5 MB
Last updated
almost 5 years ago
docker pull bioliquidator/bamliquidator