search

human-pangenomics / HPP_Year1_Data_Freeze_v1.0

48 stars 4 forks source link

Guidance for Bionano data visualization #3

Closed sachalau closed 2 years ago

sachalau commented 2 years ago

Dear human pangenomics consortium,

Thank you so much for putting such a wealth of data into the public domain ! I've used the PacBio data to investigate CNV on the STRC-STRCP1 locus, and how we can detect them using the PacBio data. FYI I extracted the reads on these regions then assembled the data with HifiASM to reconstruct the two haplotypes.

Doing so, I identified an heterozygous deletion of CKMT1B-STRC-CATSPER2 on HG02630 (on NA019240 as well, which was well known, see: http://dgv.tcag.ca/gb2/gbrowse_details/dgv2_hg19?ref=chr15;start=43845410;end=44024490;name=gssvL39070;class=Sequence;feature_id=15307;db_id=hg19_dgvgold%3Adatabase). Then I would be very interested to check that the BioNano data shows the same deletion. However, I'm not able to access Bionano proprietary software analysis and visualization tools.

I've seen that you refer to the BioNano website regarding the visualization and analysis of their data, but I was wondering if you have specific tips for open access tools in order to visualize the information on this specific region (15q15.3) for this sample?

Thanks a lot for your help

juklucas commented 2 years ago

Bionano access has a genome viewer and mapper integrated: https://bionanogenomics.com/support-page/bionano-access-software/. It is free and can be installed locally. Hope this helps.

sachalau commented 2 years ago

Thanks for the answer ! Indeed donwloading BioNano Access is free after redeeming its personal information to BioNano, I'll try to convert the cmap file into an "Alignment" from the CLI tool and visualize the result with BioNano Access.

Edit: I've managed ! I could perform the Map Alignment and visualize the region on BioNano Access, confirming the deletion seen with HiFi data. Thanks a lot for your help.

juklucas commented 2 years ago

Glad to hear it!