7
votes
Accepted
Hosting IGV web on a server
You can use X11 forwarding to run IGV on the headless server where the data is located and simply forward the GUI to your client machine using the X11 protocol. This is a solution I use consistently ...
- 1,149
7
votes
How to show only my read on IGV?
Partially a shameless plug... I've written a genome browser, ASCIIGenome, entirely controlled through the command line. As such, it makes relatively easy to deal with questions like yours. For example,...
- 689
5
votes
Accepted
What does the IGV refseq genes with three different thicknesses of lines mean?
The thinkness indicates whether something is an intron, a coding exon, or a UTR. The very thin lines are introns, the full thickness boxes are coding exons and the thinner boxes are UTRs.
UTRs, ...
- 9,677
5
votes
Accepted
How to create a .bed file from .fasta?
Here is a fun little python script I cooked up for the occasion. It will take a standard fasta file as a command-line argument and turn it into the proper bed format. Using your example fasta:
...
- 631
5
votes
Accepted
What do the read colors in IGV mean?
Could it be that these are reads with their mates found on other chromosomes? That's the part of the IGV documentation which seems to make sense in this context:
for paired end reads that are coded ...
- 2,086
4
votes
How to create a .bed file from .fasta?
I'm assuming the FASTA header contains all the information you want. You can easily generate a proper bed file with Biopython:
...
- 3,928
4
votes
Accepted
How can I export a full alignment from IGV as an image?
Running an IGV batch script helps increase the number of reads per image, compared with File | Save image, but it does not solve the issue by itself.
To run a ...
- 839
3
votes
How can I not show insertions in the Integrative Genome Viewer (IGV)?
Preferences -> Alignments -> Hide indels < 'x' bases.
Credit to Pierre Lindenbaum
- 1,149
3
votes
Accessing .bam/.cram files from AWS S3?
You could set up a public read-only bucket in an S3 account and put your files there. URLs would look like:
https://${username}.s3.amazonaws.com/public/${filename}
...
- 3,125
3
votes
Why does IGV turn a VCF QUAL of "." into -10?
Looks like they are treating the "." as a value of 1. According to the VCF spec the quality is "−10log10 prob". Where are you getting your QUALs from? I have never seen the quals as a "." and IGV ...
- 2,574
3
votes
How to create a .bed file from .fasta?
If your headers are always of the form >chrZ:a-b, where chrZ is a chromosome name, a is a ...
- 3,125
3
votes
How to create a .bed file from .fasta?
The UCSC format you linked to isn't a BED file, your method should never produce it. What you posted as your desired output is also not a BED file. Below is a BED file:
...
- 19.6k
2
votes
Accepted
IGV jump to rsID location
Yes, if you load the list you are interested in as a non-indexed "BED" file then you can jump to an rsID or any other name in the BED file. You'll need a targeted list, dbSNP for example is much too ...
- 56
2
votes
How to create a .bed file from .fasta?
Assuming that you have a reference genome sequence file (e.g., reference.fasta) available. Getting this kind of file is straightforward.
1) Index the reference ...
- 873
2
votes
Accepted
How to visualize called narrowPeak files in UCSC Genome browser or IGV?
I think you might have changed the separator (or at least have some kind of inconsistency from the required format) for your file. Note that peak output files from MACS2 are variants of BED files.
It ...
- 1,573
2
votes
Loading local FASTA file in igv.js
It looks as though the script is looking for a URL (fastaURL) so you could try specifying the file as file://directory/test.fasta
By default though, javascript cannot read local files from disk for ...
- 1,012
2
votes
Searching for HLA-B in DNA results
Typical SNP calling wouldn't give you good results on classical HLA genes. Ignore the VCF. Try a dedicated HLA genotyper on raw reads instead. I heard optitype is a good one for exome or whole-genome ...
- 6,485
1
vote
Searching for HLA-B in DNA results
The specific question and the easiest question is the absence of HLA-B*15:01 from your sample and that is not unexpected at all.
The maximum frequency of this allele is 40% found in "China ...
M__♦
- 11.9k
1
vote
What does presence/absence of black lines mean in IGV?
Black line represents an indel. Read was lengthened to fit consensus.
No black line (blank), no read/sequence. Read likely ended or was truncated.
- 221
1
vote
Accepted
How can I convert codon coordinates to genomic position?
HFE|LOC108783645 is https://www.ncbi.nlm.nih.gov/gene/108783645. You can use biomaRt to go from the LOCxxxx ID to location. ...
- 2,086
1
vote
Accessing .bam/.cram files from AWS S3?
I have recently open sourced a Java NIO SPI for S3 that allows direct reads from S3 using Java applications that use the NIO model. This allows applications like GATK and some parts of Picard to ...
- 141
1
vote
Accessing .bam/.cram files from AWS S3?
Doo you have your heart set on AWS, or are you open to using Google Cloud Platform (GCP)?
If you're open to using GCP, there are some advantages. For example GATK can read and write directly to and ...
1
vote
Hosting IGV web on a server
obviously I'm late but if this is still an open question open an issue in one of our github projects,
github.com/igvteam/igv (Java desktop),
github.com/igvteam/igv.js (pure javascript component),
...
- 56
1
vote
Hosting IGV web on a server
One possibility might be to put the full IGV application on the server, and use the igvR package in R on the server to access the IGV API. You could then use R plotting facilities etc to show your ...
- 1,012
1
vote
Hosting IGV web on a server
According to their discription
igv-webapp is a pure-client "genome browser" application based igv.js.
Pure-client, so it will be difficult to let it display tracks that are on the server itself. ...
1
vote
Loading local FASTA file in igv.js
just stumbled on this. I'm the developer of igv.js. Please feel free to open issues and questions on our git forum, I don't often have time to browse other forums.
Browsers will not allow loading ...
- 56
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