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--- 4dn:phase1:nofic_steering_committee:analysis_products [2020/05/07 20:25]
Ran
+++ 4dn:phase1:nofic_steering_committee:analysis_products [2025/04/22 16:21] (current)
@@ Line 11: / Line 11: @@
 *** 28 Mar 2020 ***
-**Processed embeddings:**
+**Processed embeddings [Noble Lab]:**
 Here we used three different approaches to calculate similarity/distance between Hi-C matrices:
@@ Line 20: / Line 20: @@
 scHiCluster: [[https://data.4dnucleome.org/files-processed/4DNFIKTK5Z1U/|https://data.4dnucleome.org/files-processed/4DNFIKTK5Z1U/]]
-Plots of 2D embeddings with CDP, HiCRep and scHiCluster:
-**{{https://lh5.googleusercontent.com/hw9d-nP_ZHz8_jH9Pd9391JA2_-d5bLNUJNH6JnOB7niUKwa3upPT5s475YdpY33QTNdufhRjL1lH9Yh-oYhopuogxvIFyVbSmq-6ku8JHZPEMf9bshW-wsxBktxSK7yuoysKfGTP-M?nolinkx249px;}}** **{{https://lh5.googleusercontent.com/otBNSUIQZ2wPkNW6r0pZcm6e0maEZ8tRnNs3ngfRohYzM5xnhZcEc22GXIXvO7-tsH21XaPnwBYCwAuG7RV0h71eIFAnix4AVRN2uuBupQ3qHGA5ZAPAX42l9f4ZR_wqSN_KspQbmjw?nolinkx249px;}}{{https://lh4.googleusercontent.com/fpRt-BFzCEyijdP_K_ftI9JL5GXf3_nenlBvXrPW5e39dTMSd8xQCrzhmX2xJkB8Oqpww6FG1PdtpitL-Vq62yyjazoTlkxivKduRHA2041ayJ0fxSNwpLsVcIV9qB0t__RRBKDSKTM?nolinkx249px;}}** **{{https://lh6.googleusercontent.com/IMzWgPTsmbCx_yLV-fjL3gZReQJws9EbBRJPJ4WscSXes64YUsLSut5Ixalf9ZUME-Lg2XSFdc5yk_locXObKtSdcmtr7kwpjiKWYx0nRWsi1u9D_bS1RZYP2MsraQ1PLLEQxsSVHro?nolinkx98px;}}**
 *** 07 May 2020 ***
@@ Line 31: / Line 27: @@
 ===== 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 37: / 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 55: / 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 63: / 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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