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4dn:phase1:nofic_steering_committee:analysis_products
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4dn:phase1:nofic_steering_committee:analysis_products [2020/05/07 20:35] Ran [scHi-C data (Ren)] |
4dn:phase1:nofic_steering_committee:analysis_products [2025/04/22 16:21] (current) |
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| scHiCluster: [[https://data.4dnucleome.org/files-processed/4DNFIKTK5Z1U/|https://data.4dnucleome.org/files-processed/4DNFIKTK5Z1U/]] | scHiCluster: [[https://data.4dnucleome.org/files-processed/4DNFIKTK5Z1U/|https://data.4dnucleome.org/files-processed/4DNFIKTK5Z1U/]] | ||
| - | |||
| - | Plots of 2D embeddings with CDP, HiCRep and scHiCluster: | ||
| *** 07 May 2020 *** | *** 07 May 2020 *** | ||
| ---- | ---- | ||
| - | |||
| ===== scHi-C data (Ren) ===== | ===== scHi-C data (Ren) ===== | ||
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| ---- | ---- | ||
| - | |||
| ===== haplotype analysis (Gilbert and Ren) ===== | ===== haplotype analysis (Gilbert and Ren) ===== | ||
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| ===== haplotype analysis (Rafelski) ===== | ===== 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. | 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. | ||
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| [[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/]] | [[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: ===== | ===== Working with mcool files: ===== | ||
4dn/phase1/nofic_steering_committee/analysis_products.1588908904.txt.gz · Last modified: 2025/04/22 16:21 (external edit)