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igvteam / igv-notebook

Module for embedding igv.js in an IPython notebook
MIT License
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Just to confirm, could you explain if the data of my BAM files are analysed locally while using this wonderful library. #28

Closed Manuel-DominguezCBG closed 8 months ago

Manuel-DominguezCBG commented 8 months ago

My command looks like this

image 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': './COSMIC.bam', 'indexPath': './COSMIC.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. 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.

jrobinso commented 8 months ago

It is all local. igvjs is a pure client app, it runs in your browser

Sent from Gmail Mobile

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.

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv-notebook/issues/28, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHD2HH6LODUDW3X5CA7EVTYF62CLAVCNFSM6AAAAAA7YIFKG2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGAYDQNZYGA2TKOA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

jrobinso commented 8 months ago

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.

Manuel-DominguezCBG commented 8 months ago

Thank you soo much for your prompt replay and thanks for this wonderful tool. I close this 👍