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Questions tagged [bigwig]

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2 votes
0 answers
24 views

How come bigWigSummary shows coverage greater than 1 for some region of the genome?

I am running this command, using the UCSC utilities: bigWigSummary -type=coverage ./galGal6.phastCons77way.bw chr4 25526708 25528708 1 to get phastCons77way ...
VeritatemAmo's user avatar
0 votes
1 answer
315 views

RNA seq .counts.txt to bigwig conversion

I've downloaded neuronal RNA seq data from GEO. The files are in .counts.txt format. Could I convert them to bigwig? If so, how?
Samir's user avatar
  • 1
2 votes
2 answers
529 views

How to convert BAM file to bigWig in Python?

I am manipulating some BAM files using pysam package which seems to be very fast and handy. However, I ran into problem when I am trying to generate bigWig files ...
Phoenix Mu's user avatar
1 vote
1 answer
154 views

BigWig circular plot representation

I would like to ask if anyone knows or has experience in representing BigWig signals in a circular plot? I mean like IGV but in circular plot not linear. Or any library that can be used in plotting ...
Abed Kurdi's user avatar
1 vote
0 answers
147 views

Question: UCSC hub: autoscale option for multiwig track

I am making a hub on UCSC Genome Browser and I am aiming to display multiple bigWig files as a single track (multiwig container). I decided to use the autoscale option because I wanted a dynamic scale:...
mf94's user avatar
  • 203
2 votes
0 answers
122 views

Which data format for stranded coverage data

I need tools I am writing to output data in terms of score for each base in the genome. The format needs to be indexed for fast random access. The obvious choices are bigWig and tabix-index bedgraph ...
Ian Sudbery's user avatar
  • 3,321
0 votes
2 answers
1k views

Is there a standard method to validate whether a bigWig file is correct?

I have a bigWig file of extension *.bw (which is standard), but I am suspicious that this file may be of an incorrect format. Is there a standard method in the ...
ShanZhengYang's user avatar
2 votes
2 answers
3k views

bigWig to bed for regions above/below threshold

I'd like to threshold a bigWig file on a value and get all regions above or below that value in bed format. Ideally without too many file conversions. Are there any tools to do that?
isthisthat's user avatar
4 votes
1 answer
392 views

Adding entries to bigwig file

I generate bigwig files using a shell script based on bedtools genomecov (to generate a bedgraph from a bam file) bedmap (to ...
bli's user avatar
  • 3,130
3 votes
1 answer
154 views

IGV faster loading remote bigWig files

I noticed remote bigWig files (http URL) take sometimes about 1 minute to load on IGV. Once they loaded, jumping from one region to another can also take several seconds. My understanding is that ...
719016's user avatar
  • 2,324
3 votes
1 answer
309 views

Time and memory efficient processing of many intervals for a bigWig file

I am trying to calculate the mappability adjusted length of introns as described by Boutz et al. Briefly, for each intron I wish to calculate the length minus the number of bases that are non-...
Ian Sudbery's user avatar
  • 3,321
5 votes
1 answer
547 views

Customizing bigWig file

I generate bigWig files using bamCoverage from deeptools, in part for my colleagues to visualize their mapped libraries in the IGV viewer. A problem is that the ...
bli's user avatar
  • 3,130
7 votes
1 answer
853 views

What unit do I get on the y-axis of a metagene profile plot?

I start with a sorted and indexed bam file ("mapped.bam") representing the mapping of small reads on a reference genome, and a bed file ("genes.bed") containing the coordinates of a set of features of ...
bli's user avatar
  • 3,130