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4dn:phase1:working_groups:omics_data_standards:minutes-10-24-2016
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4dn:phase1:working_groups:omics_data_standards:minutes-10-24-2016 [2019/02/15 09:09] oh |
4dn:phase1:working_groups:omics_data_standards:minutes-10-24-2016 [2025/04/22 16:21] (current) |
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| Anisogenic biological replicate: same cell type from different individuals.\\ Isogenic biological replicate: same cell type from same individual, separate cultures.\\ Technical replicate: same culture, library prepared separately.\\ ENCODE dropped “biological replicates” and use “isogenic replicates” universally. (there are non-isogenic biological replicates, which may have worse reproducibility though) | Anisogenic biological replicate: same cell type from different individuals.\\ Isogenic biological replicate: same cell type from same individual, separate cultures.\\ Technical replicate: same culture, library prepared separately.\\ ENCODE dropped “biological replicates” and use “isogenic replicates” universally. (there are non-isogenic biological replicates, which may have worse reproducibility though) | ||
| - | * | + | * For HiC we will need two biological replicates (independently grown / engineered / manipulated). Both isogenic and non-isogenic replicates count toward biological replicates although isogenic ones are more desired. (no recommendations, see below) |
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| - | For HiC we will need two biological replicates (independently grown / engineered / manipulated). Both isogenic and non-isogenic replicates count toward biological replicates although isogenic ones are more desired. (no recommendations, see below) | + | |
| * Non-isogenic information is not incorporated in metadata yet. Needs to make it more explicit to data generating and submitting groups. | * Non-isogenic information is not incorporated in metadata yet. Needs to make it more explicit to data generating and submitting groups. | ||
| * Would non-isogenic samples be actually more beneficial because of the variability? However, isogenic samples are still needed to see how large the non-isogenic part is in the differences. We probably don’t recommend isogenic or non-isogenic and leave that decision to data submitters. | * Would non-isogenic samples be actually more beneficial because of the variability? However, isogenic samples are still needed to see how large the non-isogenic part is in the differences. We probably don’t recommend isogenic or non-isogenic and leave that decision to data submitters. | ||
| - | * | + | * There may be cases when only one clone is available so we may need to just recommend two biological replicates instead of requiring them |
| - | + | * Such recommendation / requirements may also need to coordinate with imaging groups to meet their imaging needs | |
| - | There may be cases when only one clone is available so we may need to just recommend two biological replicates instead of requiring them | + | |
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| - | Such recommendation / requirements may also need to coordinate with imaging groups to meet their imaging needs | + | |
| Sequencing Depth | Sequencing Depth | ||
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| * Some metrics still apply, such as number of PCR duplicates and unmappable reads | * Some metrics still apply, such as number of PCR duplicates and unmappable reads | ||
| * Distributions of such parameters may be used after accepting data to establish a standard | * Distributions of such parameters may be used after accepting data to establish a standard | ||
| - | * | + | * Better to phrase this as a recommendation as lots of groups still cannot reach 500M raw reads/replicate? |
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| - | Better to phrase this as a recommendation as lots of groups still cannot reach 500M raw reads/replicate? | + | |
| * Groups may make an effort to meet such standard once it’s determined and it’s doable with current technology. | * Groups may make an effort to meet such standard once it’s determined and it’s doable with current technology. | ||
| * If 500M is the typical number of reads per sample, the low bar needs to be less than that. (for example, 400M/replicate) | * If 500M is the typical number of reads per sample, the low bar needs to be less than that. (for example, 400M/replicate) | ||
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| * Selection may be employed to select for datasets with enough reads for loop calling, etc. | * Selection may be employed to select for datasets with enough reads for loop calling, etc. | ||
| * We can start by recommending 500M/replicate x 2 replicates and having 400M/replicate x 2 as a requirement and establishing a higher tier for loop-calling datasets. | * We can start by recommending 500M/replicate x 2 replicates and having 400M/replicate x 2 as a requirement and establishing a higher tier for loop-calling datasets. | ||
| - | * | + | * May need to share this requirement / recommendation to other groups among 4DN Network for comments. |
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| - | May need to share this requirement / recommendation to other groups among 4DN Network for comments. | + | |
| </WRAP>~~TABLE_CELL_WRAP_STOP~~| | </WRAP>~~TABLE_CELL_WRAP_STOP~~| | ||
4dn/phase1/working_groups/omics_data_standards/minutes-10-24-2016.1550250558.txt.gz · Last modified: 2025/04/22 16:21 (external edit)