# 24Q2 - PureCN Integer Copy Number for Chr X and Y

**URL:** <https://forum.depmap.org/t/24q2-purecn-integer-copy-number-for-chr-x-and-y/3575>\
**Category:** Q&A\
**Tags:** omics\
**Created:** [September 12, 2024, 12:04am UTC](https://forum.depmap.org/t/24q2-purecn-integer-copy-number-for-chr-x-and-y/3575 "2024-09-12T00:04:06Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![Sanjana\_Srinivasan](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/sanjana_srinivasan/32/1127_2.png) [@Sanjana\_Srinivasan](https://forum.depmap.org/u/Sanjana_Srinivasan)\
**Post date:** [September 12, 2024, 12:04am UTC](https://forum.depmap.org/t/24q2-purecn-integer-copy-number-for-chr-x-and-y/3575/1 "2024-09-12T00:04:06Z")

</div>

Hello,

I am looking through the data release in 24Q2 and notice that the PureCN copy number profiles for both genes and segments do not have data for chromosome X and Y.  
Is there somewhere I can find this data? Is there a way to calculate allele specific copy number from the relative copy number files?

Thank you very much!

---

<div class="post-metadata">

**Author:** ![simz](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/simz/32/440_2.png) [@simz](https://forum.depmap.org/u/simz)\
**Post date:** [September 19, 2024, 6:28pm UTC](https://forum.depmap.org/t/24q2-purecn-integer-copy-number-for-chr-x-and-y/3575/2 "2024-09-19T18:28:47Z")

</div>

Hi,

Thanks for reaching out. We’re currently looking into this issue and evaluating other absolute copy number callers. In the meantime, for absolute copy number calls, there is one named  
CCLE\_ABSOLUTE\_combined\_20181227 from the CCLE (2019) project that’s available on the portal. However, it does contain less cell lines than the PureCN dataset.

Thanks,  
Simone

---

<div class="post-metadata">

**Author:** ![wangc90](https://avatars.discourse-cdn.com/v4/letter/w/6f9a4e/32.png) [@wangc90](https://forum.depmap.org/u/wangc90)\
**Post date:** [April 6, 2025, 6:21pm UTC](https://forum.depmap.org/t/24q2-purecn-integer-copy-number-for-chr-x-and-y/3575/3 "2025-04-06T18:21:31Z")

</div>

Hi Sanjana,

I have the similar question as your’s. I am wondering have you figured out where to get the copy number for the sex chromosomes.

thanks

---

<div class="post-metadata">

**Author:** ![wangc90](https://avatars.discourse-cdn.com/v4/letter/w/6f9a4e/32.png) [@wangc90](https://forum.depmap.org/u/wangc90)\
**Post date:** [April 6, 2025, 6:21pm UTC](https://forum.depmap.org/t/24q2-purecn-integer-copy-number-for-chr-x-and-y/3575/4 "2025-04-06T18:21:37Z")

</div>

I couldn’t find the absolute copy number calls for sex chromosomes in DepMap Public 24Q4 OmicsAbsoluteCNSegmentsProfile.csv. I am wondering where I can find them in any previous release?

thank you