BAM slicing from legacy archive

[pbousquets]

Hi! I'm trying to figure out if it's possible to download bam slices for legacy archive. I've tried this simple command to download BRCA1 and BRCA2 regions from a random case: bamfile = slicing("46c365e2-d78e-45ed-8356-c9ad57629c34", symbols=c("BRCA1", "BRCA2"),token=token, legacy = T) which returns: Error in .gdc_post(endpoint = sprintf("legacy/slicing/view/%s", uuid), : Not Found (HTTP 404).

[ilianapeneva]

Hello, I am getting the same error when trying to download bam slices from the legacy archive. I tried downloading them without VPN but it still gives me the same error. Could it be because the API URL has been changed? My session info is below:

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /gpfs3/apps/eb/skylake/software/OpenBLAS/0.3.7-GCC-8.3.0/lib/libopenblas_skylakexp-r0.3.7.so

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.4.0             stringr_1.4.0            
 [3] dplyr_0.8.3               purrr_0.3.3              
 [5] readr_1.3.1               tidyr_1.0.0              
 [7] tibble_2.1.3              ggplot2_3.2.1            
 [9] tidyverse_1.3.0           GenomicDataCommons_1.15.0
[11] magrittr_1.5             

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3                  lubridate_1.7.4            
 [3] lattice_0.20-38             assertthat_0.2.1           
 [5] zeallot_0.1.0               R6_2.4.1                   
 [7] GenomeInfoDb_1.22.1         cellranger_1.1.0           
 [9] backports_1.1.5             reprex_0.3.0               
[11] stats4_3.6.2                httr_1.4.1                 
[13] pillar_1.4.2                zlibbioc_1.32.0            
[15] rlang_0.4.2                 lazyeval_0.2.2             
[17] readxl_1.3.1                rstudioapi_0.10            
[19] S4Vectors_0.24.4            Matrix_1.2-18              
[21] BiocParallel_1.20.1         RCurl_1.95-4.12            
[23] munsell_0.5.0               DelayedArray_0.12.3        
[25] broom_0.5.3                 compiler_3.6.2             
[27] modelr_0.1.5                pkgconfig_2.0.3            
[29] BiocGenerics_0.32.0         tidyselect_0.2.5           
[31] SummarizedExperiment_1.16.1 GenomeInfoDbData_1.2.2     
[33] IRanges_2.20.2              matrixStats_0.55.0         
[35] fansi_0.4.0                 withr_2.1.2                
[37] crayon_1.3.4                dbplyr_1.4.2               
[39] bitops_1.0-6                rappdirs_0.3.3             
[41] grid_3.6.2                  nlme_3.1-143               
[43] jsonlite_1.6                gtable_0.3.0               
[45] lifecycle_0.1.0             DBI_1.1.0                  
[47] scales_1.1.0                cli_2.0.0                  
[49] stringi_1.4.3               XVector_0.26.0             
[51] fs_1.3.1                    xml2_1.2.2                 
[53] generics_0.0.2              vctrs_0.2.0                
[55] tools_3.6.2                 Biobase_2.46.0             
[57] glue_1.3.1                  hms_0.5.2                  
[59] parallel_3.6.2              colorspace_1.4-1           
[61] GenomicRanges_1.38.0        rvest_0.3.5                
[63] haven_2.2.0                

[LiNk-NY]

Hi @ilianapeneva @pbousquets

It seems like slicing unharmonized BAM files in the GDC Legacy Portal is not supported. See here for more info https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/

And perhaps the API has changed but I have no way to test (no auth token).

Note. I've updated the documentation and the links to reflect above points.

Best regards, Marcel