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--- 4dn:phase1:nofic_steering_committee:analysis_products [2020/05/07 17:57]
Ran [sci-Hi-C data (Shendure)]
+++ 4dn:phase1:nofic_steering_committee:analysis_products [2025/04/22 16:21] (current)
@@ Line 9: / Line 9: @@
 **mcool files:** [[https://noble.gs.washington.edu/~ranz0/4DN/wtc11/results/shendure-lab/mcool/|https://noble.gs.washington.edu/~ranz0/4DN/wtc11/results/shendure-lab/mcool/]]. For details please refer to notebook [[https://noble.gs.washington.edu/~ranz0/4DN/wtc11/results/ranz0/results.html#Process_sciHi-C_to_mcool_format|https://noble.gs.washington.edu/~ranz0/4DN/wtc11/results/ranz0/results.html#Process_sciHi-C_to_mcool_format]]
-Mar 2020
+*** 28 Mar 2020 ***
-**Processed embeddings:**
+**Processed embeddings [Noble Lab]:**
-Here we used three different approaches to calculate similarity/distance between Hi-C matrices, For contact decay profile, only
+Here we used three different approaches to calculate similarity/distance between Hi-C matrices:
-Contact decay profile: [[https://data.4dnucleome.org/files-processed/4DNFIHA69V3Y/|https://data.4dnucleome.org/files-processed/4DNFIHA69V3Y/]]
+Contact decay profile: [[https://data.4dnucleome.org/files-processed/4DNFIHA69V3Y/|https://data.4dnucleome.org/files-processed/4DNFIHA69V3Y/]]. CDP by 500kb bins, similarity matrix is calculated as cosine similarity of log-scaled bins. Distance matrix is calculated as sqrt(2-2*similarity) and 2D embeddings are generated by multidimensional scaling.
-HiCRep: https://data.4dnucleome.org/files-processed/4DNFIPX8D8DX/
+HiCRep: [[https://data.4dnucleome.org/files-processed/4DNFIPX8D8DX/|https://data.4dnucleome.org/files-processed/4DNFIPX8D8DX/]]. Calculate pairwise similarity by HiCRep (Yang et al. 2017). Distance matrix is calculated as sqrt(2-2*similarity) and 2D embeddings are generated by multidimensional scaling.
-scHiCluster: https://data.4dnucleome.org/files-processed/4DNFIKTK5Z1U/
+scHiCluster: [[https://data.4dnucleome.org/files-processed/4DNFIKTK5Z1U/|https://data.4dnucleome.org/files-processed/4DNFIKTK5Z1U/]]
-----
+*** 07 May 2020 ***
+----
 ===== scHi-C data (Ren) =====
-scHi-C script and processed files provided by [[https://4dn.slack.com/team/UU1HZACHK|@Yanxiao Zhang]] in the Ren lab:
+scHi-C script and processed files provided by [[https://4dn.slack.com/team/UU1HZACHK|@Yanxiao Zhang]] **[Ren Lab]**:
 **Script**: [[https://github.com/ren-lab/hic-pipeline/blob/master/scripts/Snakefile|https://github.com/ren-lab/hic-pipeline/blob/master/scripts/Snakefile]] with the rule scHiC. Please note that since the pipeline is still under development the documentation is not complete.
@@ Line 32: / Line 33: @@
 **Processed files**: [[http://renlab.sdsc.edu/yanxiao/Miao_data/scHiC/data/Xiaomeng_data/useful_contacts/|http://renlab.sdsc.edu/yanxiao/Miao_data/scHiC/data/Xiaomeng_data/useful_contacts/]]\\ Please use the *.valid_pairs.rm_hotspot.sorted.txt.gz. The column names are (1) read name (2) chr1 (3) position 1 (4) bin1 (5) chr2 (6) pos2 (7) bin2
-Mar 2020
+*** 28 Mar 2020 ***
+**Processed embeddings:**** [Noble Lab]**
+Here we used three different approaches to calculate similarity/distance between Hi-C matrices:
+Contact decay profile: [[https://data.4dnucleome.org/files-processed/4DNFIGLS3JZN/?redirected_from=%2F4DNFIGLS3JZN%2F|https://data.4dnucleome.org/files-processed/4DNFIGLS3JZN/?redirected_from=%2F4DNFIGLS3JZN%2F]]. CDP by 500kb bins, similarity matrix is calculated as cosine similarity of log-scaled bins. Distance matrix is calculated as sqrt(2-2*similarity) and 2D embeddings are generated by multidimensional scaling.
+HiCRep: [[https://data.4dnucleome.org/files-processed/4DNFIPX8D8DX/|https://data.4dnucleome.org/files-processed/4DNFIHM5K63H/]]. Calculate pairwise similarity by HiCRep (Yang et al. 2017). Distance matrix is calculated as sqrt(2-2*similarity) and 2D embeddings are generated by multidimensional scaling.
+scHiCluster: [[https://data.4dnucleome.org/files-processed/4DNFIKTK5Z1U/|https://data.4dnucleome.org/files-processed/4DNFI488OK8H/]]
+*** 07 May 2020 ***
 ----
@@ Line 50: / Line 63: @@
 ===== haplotype analysis (Rafelski) =====
-From Ru Gunawardane:
+**[Ru Gunawardane]:**
 We have parental WTC-11 linked read (10X) and short read whole genome data, and it is available as two packages through quilt ([[https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.quiltdata.com%2Finstallation&data=02%7C01%7C%7C0a610651a1014473e27a08d7d26adcac%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C637209228714084680&sdata=6mZztNIU0nWSIgXqKJ2%2BKX%2FdMXGzbSklTTM%2Bgde%2BnSY%3D&reserved=0|https://docs.quiltdata.com]]). These packages include both raw and aligned reads, variant calls, and **phasing** for linked read data.
@@ Line 58: / Line 71: @@
 [[https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopen.quiltdata.com%2Fb%2Fallencell%2Ftree%2Faics%2Fwtc11_short_read_genome_sequence%2F&data=02%7C01%7C%7C0a610651a1014473e27a08d7d26adcac%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C637209228714094625&sdata=KVUFOEVY3gGPnC5RPNLHx1M%2BY7l1arLHlDIFgtlElLk%3D&reserved=0|https://open.quiltdata.com/b/allencell/tree/aics/wtc11_short_read_genome_sequence/]]
-Mar 28 2020
+*** Mar 28 2020 ***
 ----
 ===== Working with mcool files: =====

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