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bam2wig specifications

Information


Unique identifier OMICS_19257
Name bam2wig
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data An DNA sequence alignment.
Input format bam
Output data A coverage file.
Output format WIG, BigWig
Operating system Unix/Linux, Mac OS
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.4
Stability Stable
Requirements
SAMtools, wigToBigWig
Registration required No
Maintained Yes

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Documentation


Maintainer


  • person_outline Michael J. Axtell

bam2wig citations

 (13)
library_books

Innate Immune Response and Off Target Mis splicing Are Common Morpholino Induced Side Effects in Xenopus

2018
Dev Cell
PMCID: 5861998
PMID: 29478923
DOI: 10.1016/j.devcel.2018.01.022

[…] merged using samtools v1.3.1 () and converted to the bigWig format. These genome tracks were normalized to the wigsum of 1 billion excluding any reads with mapping quality <10 using the python script bam2wig.py from RSeQC v2.6.4 (). Tracks were visualized in the IGV genome browser v2.3.92 (). […]

library_books

Decoding the dynamic DNA methylation and hydroxymethylation landscapes in endodermal lineage intermediates during pancreatic differentiation of hESC

2018
Nucleic Acids Res
PMCID: 5888657
PMID: 29394393
DOI: 10.1093/nar/gky063

[…] ended). Single-end reads were mapped to GRCh37/hg19 assembly using bsmap with the ‘-v 2 -n 1 -q 3 -r 0’ parameter. Duplicate reads were treated using macs2 filterdup with the ‘–keep-dup 2’ parameter. Bam2wig.py in RSeQC was used to transform the bam file to normalized bigWig files with the parameter ‘-t 2000000000’. Finally, the combined tracks for UCSC Genome Browser were generated. Macs2 was use […]

library_books

Pancreatic gene expression during recovery after pancreatitis reveals unique transcriptome profiles

2018
Sci Rep
PMCID: 5780441
PMID: 29362419
DOI: 10.1038/s41598-018-19392-0

[…] een genders, the recovery time was adjusted as a covariate. RNA-seq mapping statistics are provided in Supplementary Table .The alignment results (bam files) were converted to bigWig format using the bam2wig tool of RSeQC, for the visualization of read coverage in Integrated Genomics Viewer (IGV) genome browser. The total read coverage of each sample was normalized to 10Mbp, so that the peaks of d […]

library_books

Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction

2017
BMC Genomics
PMCID: 5483258
PMID: 28646875
DOI: 10.1186/s12864-017-3860-x

[…] ce = false --min_intron_len = 8, version: 2.7) using the hints from the mapping result of the RNA-seq (bam2hints with options --intronsonly --maxgaplen = 0 --minintronlen = 8 --maxintronlen = 10,000, bam2wig and wig2hints.pl with options --width = 10 --margin = 10 --minthresh = 2 --minscore = 4 --prune = 0.1 --radius = 4.5 were used to prepare the hints and the configuration file “extrinsic.M.RM.E […]

library_books

Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes

2017
Nat Commun
PMCID: 5467160
PMID: 28585529
DOI: 10.1038/ncomms15708

[…] The resulting single BAM file was used as input for bam2hints.pl provided by AUGUSTUS to create intron part hints (option --I). To create exon part hints, BAM files were converted to WIG files using bam2wig and used to generate the hint file using wig2hints.pl. The structural annotation and information on transcript evidence of the 53,190 predicted WB42 genes is available in the file WB42_v2.gff3 […]

library_books

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

2017
PLoS Biol
PMCID: 5393560
PMID: 28414715
DOI: 10.1371/journal.pbio.2001069

[…] Wig files were generated using the bam2wig script [] and were normalized by the number of mapped reads divided by 107. DNase I signal is represented using the first position of the read alignments considered as the cutting position and […]

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