search

bioinform / somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq
http://bioinform.github.io/somaticseq/
BSD 2-Clause "Simplified" License
192 stars 53 forks source link

Where are the 10x Genomics single-cell copy number variation (CNV) analysis results? #120

Closed genetronhealth closed 1 year ago

genetronhealth commented 1 year ago

Dear SEQC-II team,

Thank you for the amazing amount of work that you have done to advance science.
In Fig. 4b and Fig. 4c of the original NBT manuscript (https://www.nature.com/articles/s41587-021-00993-6), it mentions that you have sequenced both HCC1395 and HCC1395BL at single-cell level and shows copy-number heterogeneity at single-cell level. I woud like to simulate a tumor-normal mixture at single-cell level so that the copy number of each cell at each genomic locus is preserved, and this data look perfect to me except that I cannot find the raw copy-number results files. Hence, I would like to know where to find the copy-number results generated by the cell-ranger pipeline?

yongmzhao commented 1 year ago

@genetronhealth we can provide the raw copy-number results files if you let us know your contact information. Thanks, Yongmei

zhaoxiaofei commented 1 year ago

@yongmzhao You can send the raw copy-number results to cndfeifei AT aliyun DOT com , this email is supposed to be able to receive up to 60G of attachment. You can also send a download link to this email if it is more convenient to you. Thanks!

genetronhealth commented 1 year ago

@yongmzhao

Sorry that I replied with another github account (I logged in as zhaoxiaofei using one web browser but as genetronhealth on another web brower).

Just to confirm that you can send the raw copy-number results to ( cndfeifei AT aliyun DOT com ), this email is supposed to be able to receive up to 60G of attachment. You can also send a download link to this email if it is more convenient to you. Thanks!

CNV results that look similar to the ones at https://www.10xgenomics.com/resources/datasets/colo-829-g-1-sorted-1475-cells-1-standard-1-0-0 should be fine.

Thank you!

genetronhealth commented 1 year ago

@yongmzhao Hello, is there any update on my request? If my request cannot be accomplished for any reason or if you would like to request any additional information, please let me know. Thanks.

yongmzhao commented 1 year ago

@genetronhealth I sent the files to the email address you provided. Please email me if you have further questions. Thanks.

litaifang commented 1 year ago

@genetronhealth have you gotten the files you needed?

genetronhealth commented 1 year ago

@litaifang

Yes, I got the files that I needed so far. Some CNV calling tools require alignment to GRCh37 reference, but I probably will not use all tools. I may have to ask you more question if needed.   

Thank you for sharing your files! I closed this issue.