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diff --git a/general/help/facilities.md b/general/help/facilities.md index ec2d926..f3187cf 100644 --- a/general/help/facilities.md +++ b/general/help/facilities.md @@ -72,4 +72,4 @@ All current tools are maintained on [https://gitlab.com/genenetwork/guix-bioinfo ## Cloud computing -In addition the the "bare metal" described above we increasingly use cloud services for running VMs for teaching and fallbacks, as well as for storing data, including backups. +In addition the the "bare metal" described above we increasingly use cloud services for running VMs for teaching and fallbacks, as well as for storing data, including backups. diff --git a/general/news/news.md b/general/news/news.md index 2c3e4a7..686c7a2 100644 --- a/general/news/news.md +++ b/general/news/news.md @@ -5,35 +5,35 @@ The BXD sequencing consortium has generated full genome sequence for 152 extant BXD strains. Dr. David Ashbrook has extracted the most - informative 40,000 SNPs from sequence data, and compared + informative 40,000 SNPs from sequence data, and compared sequence-based genotypes with those based on array platforms (see - entries below). In general there is excellent concordance for all but + entries below). In general there is excellent concordance for all but a handful of the BXD strains that are in widespread use (BXD1 to - BXD102). However, there are some problems and mixups that we list + BXD102). However, there are some problems and mixups that we list below. We are currently working on harmonizing data when possible, and understanding and fixing errors, when not. - This evaluation of genotypes is based on data extracted from whole-genome sequencing of BXD male spleen samples obtained in January 2017 from the Jackson Laboratory whenever possible, and from the UTHSC colony in all other cases. All animals were born between January and December 2016. + This evaluation of genotypes is based on data extracted from whole-genome sequencing of BXD male spleen samples obtained in January 2017 from the Jackson Laboratory whenever possible, and from the UTHSC colony in all other cases. All animals were born between January and December 2016. -1. BXD65b (sourced from JAX). The sequence-based genotypes correlate better to array-based 2017 genotypes of BXD65 and BXD65a than with the BXD65b array-based genotypes. It is possible that there are two somewhat distinct sub-strains now called BXD65b—one at JAX and one at UTHSC. *Recommended Action:*Sourcing BXD65b animals from JAX. +1. BXD65b (sourced from JAX). The sequence-based genotypes correlate better to array-based 2017 genotypes of BXD65 and BXD65a than with the BXD65b array-based genotypes. It is possible that there are two somewhat distinct sub-strains now called BXD65b—one at JAX and one at UTHSC. *Recommended Action:*Sourcing BXD65b animals from JAX. -2. BXD53 array-based genotypes do not correlate well with sequence-based genotypes for BXD53/2. BXD53 was rederived a second time by JAX and is now referred to formally at BXD53/2RwwJ (Stock 017749). The likely reason for the discrepancy is that we sequenced BXD53/2RwwJ (Stock 017749) rather than the older BXD53 (sourced from UTHSC) for array-based genotyping. BXD53 sequence-based genotypes correlate well with eQTL data for BXD53. *Recommended Action:*If using BXD53/2RwwJ, please obtain current sequence-based genotypes from David Ashbrook. +2. BXD53 array-based genotypes do not correlate well with sequence-based genotypes for BXD53/2. BXD53 was rederived a second time by JAX and is now referred to formally at BXD53/2RwwJ (Stock 017749). The likely reason for the discrepancy is that we sequenced BXD53/2RwwJ (Stock 017749) rather than the older BXD53 (sourced from UTHSC) for array-based genotyping. BXD53 sequence-based genotypes correlate well with eQTL data for BXD53. *Recommended Action:*If using BXD53/2RwwJ, please obtain current sequence-based genotypes from David Ashbrook. -3. BXD68 animals at UTHSC used from about 2012 to 2017 were BXD34 animals. Genotypes in the 2017 array-based file HAVE or HAVE NOT been corrected. We have corrected this error in some phenotype data sets. BXD68 from The Jackson Laboratory are genuine BXD68. We sequenced BXD68 DNA from JAX. *Recommended Action: *None unless you have used BXD68 animals obtained from UTHSC between 2012 and 2017. If so, these animals should be relabeled BXD34. +3. BXD68 animals at UTHSC used from about 2012 to 2017 were BXD34 animals. Genotypes in the 2017 array-based file HAVE or HAVE NOT been corrected. We have corrected this error in some phenotype data sets. BXD68 from The Jackson Laboratory are genuine BXD68. We sequenced BXD68 DNA from JAX. *Recommended Action: *None unless you have used BXD68 animals obtained from UTHSC between 2012 and 2017. If so, these animals should be relabeled BXD34. -4. BXD81 sequence-based genotypes correlate well with the new array-based genotypes (r = 0.81) but less well with old array-based genotypes (r = 0.66). This is presumably due to more complete inbreeding. The new sequence-based genotypes are for BXD81 sources from JAX. *Recommended Action: *None +4. BXD81 sequence-based genotypes correlate well with the new array-based genotypes (r = 0.81) but less well with old array-based genotypes (r = 0.66). This is presumably due to more complete inbreeding. The new sequence-based genotypes are for BXD81 sources from JAX. *Recommended Action: *None -5. BXD88 sequence-based genotypes do not correlate well with either of the two array-based genotype files (r = 0.50 and 0.54). Like BXD53, BXD88 was rederived a second time by JAX and is now referred to formally at BXD88/2RwwJ (Stock 007110). BXD88 was admixed at some point in the last decade that has since been rederived. BXD88/2RwwJ is only available at JAX. *Recommended Action:*Sourcing BXD88/2RwwJ from JAX; do not treat as equivalent to old BXD88. +5. BXD88 sequence-based genotypes do not correlate well with either of the two array-based genotype files (r = 0.50 and 0.54). Like BXD53, BXD88 was rederived a second time by JAX and is now referred to formally at BXD88/2RwwJ (Stock 007110). BXD88 was admixed at some point in the last decade that has since been rederived. BXD88/2RwwJ is only available at JAX. *Recommended Action:*Sourcing BXD88/2RwwJ from JAX; do not treat as equivalent to old BXD88. -6. BXD100 (JAX stock 007143) sequence-based genotypes correlates well with the older array-based genotypes (r = 0.96) but not so well with newer 2017 array data (r = 0.55). This suggests some admixture in the last decade at UTHSC that has since been fixed. *Recommended Action:*If you used BXD100s between 2006 and 2014, we recommend using genotypes from the older array-based file for this strain. If you are using new BXD100 animals sourced from JAX, then use the newer 2017 array-based genotypes or the sequence-based genotypes. +6. BXD100 (JAX stock 007143) sequence-based genotypes correlates well with the older array-based genotypes (r = 0.96) but not so well with newer 2017 array data (r = 0.55). This suggests some admixture in the last decade at UTHSC that has since been fixed. *Recommended Action:*If you used BXD100s between 2006 and 2014, we recommend using genotypes from the older array-based file for this strain. If you are using new BXD100 animals sourced from JAX, then use the newer 2017 array-based genotypes or the sequence-based genotypes. -7. BXD151 (UTHSC stock) sequence-based genotypes do not correlate with the array-based genotypes at all (r = -0.79 and -0.06). BXD151 sequence-based genotypes correlate very well with older array-based sequence for the now (formally) extinct BXD128a (r = 0.97 and 0.99 with the two array-based files). We need to check sequence of BXD151/RwwJ (JAX 029868). *Recommended Action:*None. It appears likely that BXD151 may be equivalent to what we used to call BXD128a. BXD128a is no longer officially available and we will retain the name BXD151. +7. BXD151 (UTHSC stock) sequence-based genotypes do not correlate with the array-based genotypes at all (r = -0.79 and -0.06). BXD151 sequence-based genotypes correlate very well with older array-based sequence for the now (formally) extinct BXD128a (r = 0.97 and 0.99 with the two array-based files). We need to check sequence of BXD151/RwwJ (JAX 029868). *Recommended Action:*None. It appears likely that BXD151 may be equivalent to what we used to call BXD128a. BXD128a is no longer officially available and we will retain the name BXD151. -8. BXD155 (UTHSC stock) sequence-based genotypes do not correlate with arrays (r = 0.21 and 0.18). BXD155 has an excellent correlation with previous array-based genotypes for strain BXD152 (r = 0.95 and 0.95 with arrays, 0.99 with sequence). Likely reading error or strain swap at UTHSC. BXD152 (Stock 029869, non-agouti black coat color) can be obtained from JAX, but BXD155 (gray coat color) is not yet available from JAX. *Recommended Action:*Check with David Ashbrook or Rob Williams on whether this issue has been resolved. It seems likely that the BXD155 sample that we sequenced was actually at BXD152. +8. BXD155 (UTHSC stock) sequence-based genotypes do not correlate with arrays (r = 0.21 and 0.18). BXD155 has an excellent correlation with previous array-based genotypes for strain BXD152 (r = 0.95 and 0.95 with arrays, 0.99 with sequence). Likely reading error or strain swap at UTHSC. BXD152 (Stock 029869, non-agouti black coat color) can be obtained from JAX, but BXD155 (gray coat color) is not yet available from JAX. *Recommended Action:*Check with David Ashbrook or Rob Williams on whether this issue has been resolved. It seems likely that the BXD155 sample that we sequenced was actually at BXD152. -9. BXD162 (UTHSC stock) sequence-based genotypes correlate poorly well with new array genotypes (r = 0.65 and 0.69). This strain also has a reasonable correlation with BXD170 in older array genotypes (r = 0.7). Possible admixture. BXD162 is not yet available from JAX. *Recommended Action:*Check with David Ashbrook or Rob Williams in you use this strain regarding correct nomenclature. +9. BXD162 (UTHSC stock) sequence-based genotypes correlate poorly well with new array genotypes (r = 0.65 and 0.69). This strain also has a reasonable correlation with BXD170 in older array genotypes (r = 0.7). Possible admixture. BXD162 is not yet available from JAX. *Recommended Action:*Check with David Ashbrook or Rob Williams in you use this strain regarding correct nomenclature. -10. BXD194 (UTHSC stock) sequence-based genotypes correlated with BXD87 (JAX stock) sequence-based genotypes. Probably a sample error at UTHSC when preparing samples for sequencing. We need to check the JAX BXD194/RwwJ (Stock 030878). *Recommended Action:*Check with David Ashbrook or Rob Williams in you use this strain regarding correct nomenclature. +10. BXD194 (UTHSC stock) sequence-based genotypes correlated with BXD87 (JAX stock) sequence-based genotypes. Probably a sample error at UTHSC when preparing samples for sequencing. We need to check the JAX BXD194/RwwJ (Stock 030878). *Recommended Action:*Check with David Ashbrook or Rob Williams in you use this strain regarding correct nomenclature. |