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I need to make sure that all work done is done locally. I am working with patient data. Am I sending the reads of my BAM file to IGV web and receiving in the Jupyter notebook the results of IGV web?
I don't mind if the reference genome is loaded through the internet (it is very efficient by the way well done) but my BAM files must remain local.
If you wonder why I don't just use the locally installed IGV version on my machine. I have created a Python script that automatizes the visualization of regions by using igv-notebook. My script takes the bam file and the bed file and generates a new Jupyter notebook witrh one cell in the notebook for each line found in a BED file given. This allows me to visualised straightaway all regions I want to see.
The text was updated successfully, but these errors were encountered:
Manuel-DominguezCBG
changed the title
Is possible to make run the jupyter notebook 100% locally or Am I sending the data of my BAM to IGVweb??
Just to confirm, could you explain if the data of my BAM files are analysed locally while using this wonderful library.
Nov 23, 2023
On Thu, Nov 23, 2023 at 12:57 PM Manuel Jesus Dominguez Becerra < ***@***.***> wrote:
My command looks like this
[image: image]
<https://user-images.githubusercontent.com/74112779/285305511-b2b7f16c-e36b-4de5-bb58-672a2ca054e0.png>
Here the code of that cell
print('BED line: chr3 30606853 30607004 TGFBR2_01F_P5_03')b = igv_notebook.Browser({'genome': 'hg38', 'locus': 'chr3:30606853-30607004'})b.load_track({'name': '', 'path': './SSrep1samp2_FINAL_SORTED.bam', 'indexPath': './SSrep1samp2_FINAL_SORTED.bam.bai', 'format': 'bam', 'type': 'alignment'})b.search('chr3:30606853-30607004')
I need to make sure that all work done is done locally. I am working with
patient data. I am sending the reads of my bam to IGV web and receiving in
the Jupyter notebook the results of IGV web.
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In other words nothing leaves your web browser. igv.js (embedded in igv-notebook) pulls resources such as gene annotations from remote servers, but nothing is sent the other direction.
My command looks like this
Here the code of that cell
I need to make sure that all work done is done locally. I am working with patient data. Am I sending the reads of my BAM file to IGV web and receiving in the Jupyter notebook the results of IGV web?
I don't mind if the reference genome is loaded through the internet (it is very efficient by the way well done) but my BAM files must remain local.
If you wonder why I don't just use the locally installed IGV version on my machine. I have created a Python script that automatizes the visualization of regions by using igv-notebook. My script takes the bam file and the bed file and generates a new Jupyter notebook witrh one cell in the notebook for each line found in a BED file given. This allows me to visualised straightaway all regions I want to see.
The text was updated successfully, but these errors were encountered: