This function reads in the recount3 metadata files into R. You can first
locate the files using locate_url() then download it to your computer
using file_retrieve().
read_metadata(metadata_files)A character() with the local path to recount3
metadata files.
A data.frame() with all lower case column names for the sample
metadata.
Other internal functions for accessing the recount3 data:
annotation_ext(),
create_rse_manual(),
file_retrieve(),
locate_url_ann(),
locate_url(),
project_homes(),
read_counts()
## Download the metadata files for project ERP110066
url_ERP110066_meta <- locate_url(
"ERP110066",
"data_sources/sra"
)
local_ERP110066_meta <- file_retrieve(
url = url_ERP110066_meta
)
#> 2023-05-07 00:12:41.356664 caching file sra.sra.ERP110066.MD.gz.
#> 2023-05-07 00:12:41.680826 caching file sra.recount_project.ERP110066.MD.gz.
#> 2023-05-07 00:12:42.002532 caching file sra.recount_qc.ERP110066.MD.gz.
#> 2023-05-07 00:12:42.338177 caching file sra.recount_seq_qc.ERP110066.MD.gz.
#> 2023-05-07 00:12:42.665478 caching file sra.recount_pred.ERP110066.MD.gz.
## Read the metadata
ERP110066_meta <- read_metadata(local_ERP110066_meta)
dim(ERP110066_meta)
#> [1] 1024 174
colnames(ERP110066_meta)
#> [1] "rail_id"
#> [2] "external_id"
#> [3] "study"
#> [4] "sra.sample_acc.x"
#> [5] "sra.experiment_acc"
#> [6] "sra.submission_acc"
#> [7] "sra.submission_center"
#> [8] "sra.submission_lab"
#> [9] "sra.study_title"
#> [10] "sra.study_abstract"
#> [11] "sra.study_description"
#> [12] "sra.experiment_title"
#> [13] "sra.design_description"
#> [14] "sra.sample_description"
#> [15] "sra.library_name"
#> [16] "sra.library_strategy"
#> [17] "sra.library_source"
#> [18] "sra.library_selection"
#> [19] "sra.library_layout"
#> [20] "sra.paired_nominal_length"
#> [21] "sra.paired_nominal_stdev"
#> [22] "sra.library_construction_protocol"
#> [23] "sra.platform_model"
#> [24] "sra.sample_attributes"
#> [25] "sra.experiment_attributes"
#> [26] "sra.spot_length"
#> [27] "sra.sample_name"
#> [28] "sra.sample_title"
#> [29] "sra.sample_bases"
#> [30] "sra.sample_spots"
#> [31] "sra.run_published"
#> [32] "sra.size"
#> [33] "sra.run_total_bases"
#> [34] "sra.run_total_spots"
#> [35] "sra.num_reads"
#> [36] "sra.num_spots"
#> [37] "sra.read_info"
#> [38] "sra.run_alias"
#> [39] "sra.run_center_name"
#> [40] "sra.run_broker_name"
#> [41] "sra.run_center"
#> [42] "recount_project.project"
#> [43] "recount_project.organism"
#> [44] "recount_project.file_source"
#> [45] "recount_project.metadata_source"
#> [46] "recount_project.date_processed"
#> [47] "recount_qc.aligned_reads%.chrm"
#> [48] "recount_qc.aligned_reads%.chrx"
#> [49] "recount_qc.aligned_reads%.chry"
#> [50] "recount_qc.bc_auc.all_reads_all_bases"
#> [51] "recount_qc.bc_auc.all_reads_annotated_bases"
#> [52] "recount_qc.bc_auc.unique_reads_all_bases"
#> [53] "recount_qc.bc_auc.unique_reads_annotated_bases"
#> [54] "recount_qc.bc_auc.all_%"
#> [55] "recount_qc.bc_auc.unique_%"
#> [56] "recount_qc.bc_frag.count"
#> [57] "recount_qc.bc_frag.kallisto_count"
#> [58] "recount_qc.bc_frag.kallisto_mean_length"
#> [59] "recount_qc.bc_frag.mean_length"
#> [60] "recount_qc.bc_frag.mode_length"
#> [61] "recount_qc.bc_frag.mode_length_count"
#> [62] "recount_qc.exon_fc.all_%"
#> [63] "recount_qc.exon_fc.unique_%"
#> [64] "recount_qc.exon_fc_count_all.total"
#> [65] "recount_qc.exon_fc_count_all.assigned"
#> [66] "recount_qc.exon_fc_count_unique.total"
#> [67] "recount_qc.exon_fc_count_unique.assigned"
#> [68] "recount_qc.gene_fc.all_%"
#> [69] "recount_qc.gene_fc.unique_%"
#> [70] "recount_qc.gene_fc_count_all.total"
#> [71] "recount_qc.gene_fc_count_all.assigned"
#> [72] "recount_qc.gene_fc_count_unique.total"
#> [73] "recount_qc.gene_fc_count_unique.assigned"
#> [74] "recount_qc.intron_sum"
#> [75] "recount_qc.intron_sum_%"
#> [76] "recount_qc.star.%_of_chimeric_reads"
#> [77] "recount_qc.star.%_of_chimeric_reads2"
#> [78] "recount_qc.star.%_of_reads_mapped_to_multiple_loci"
#> [79] "recount_qc.star.%_of_reads_mapped_to_multiple_loci2"
#> [80] "recount_qc.star.%_of_reads_mapped_to_too_many_loci"
#> [81] "recount_qc.star.%_of_reads_mapped_to_too_many_loci2"
#> [82] "recount_qc.star.%_of_reads_unmapped:_other"
#> [83] "recount_qc.star.%_of_reads_unmapped:_other2"
#> [84] "recount_qc.star.%_of_reads_unmapped:_too_many_mismatches"
#> [85] "recount_qc.star.%_of_reads_unmapped:_too_many_mismatches2"
#> [86] "recount_qc.star.%_of_reads_unmapped:_too_short"
#> [87] "recount_qc.star.%_of_reads_unmapped:_too_short2"
#> [88] "recount_qc.star.all_mapped_reads"
#> [89] "recount_qc.star.all_mapped_reads2"
#> [90] "recount_qc.star.average_input_read_length"
#> [91] "recount_qc.star.average_input_read_length2"
#> [92] "recount_qc.star.average_mapped_length"
#> [93] "recount_qc.star.average_mapped_length2"
#> [94] "recount_qc.star.deletion_average_length"
#> [95] "recount_qc.star.deletion_average_length2"
#> [96] "recount_qc.star.deletion_rate_per_base"
#> [97] "recount_qc.star.deletion_rate_per_base2"
#> [98] "recount_qc.star.insertion_average_length"
#> [99] "recount_qc.star.insertion_average_length2"
#> [100] "recount_qc.star.insertion_rate_per_base"
#> [101] "recount_qc.star.insertion_rate_per_base2"
#> [102] "recount_qc.star.mapping_speed,_million_of_reads_per_hour"
#> [103] "recount_qc.star.mapping_speed,_million_of_reads_per_hour2"
#> [104] "recount_qc.star.mismatch_rate_per_base,_%"
#> [105] "recount_qc.star.mismatch_rate_per_base,_%2"
#> [106] "recount_qc.star.number_of_chimeric_reads"
#> [107] "recount_qc.star.number_of_chimeric_reads2"
#> [108] "recount_qc.star.number_of_input_reads"
#> [109] "recount_qc.star.number_of_input_reads2"
#> [110] "recount_qc.star.number_of_reads_mapped_to_multiple_loci"
#> [111] "recount_qc.star.number_of_reads_mapped_to_multiple_loci2"
#> [112] "recount_qc.star.number_of_reads_mapped_to_too_many_loci"
#> [113] "recount_qc.star.number_of_reads_mapped_to_too_many_loci2"
#> [114] "recount_qc.star.number_of_reads_unmapped:_other"
#> [115] "recount_qc.star.number_of_reads_unmapped:_other2"
#> [116] "recount_qc.star.number_of_reads_unmapped:_too_many_mismatches"
#> [117] "recount_qc.star.number_of_reads_unmapped:_too_many_mismatches2"
#> [118] "recount_qc.star.number_of_reads_unmapped:_too_short"
#> [119] "recount_qc.star.number_of_reads_unmapped:_too_short2"
#> [120] "recount_qc.star.number_of_splices:_at/ac"
#> [121] "recount_qc.star.number_of_splices:_at/ac2"
#> [122] "recount_qc.star.number_of_splices:_annotated_(sjdb)"
#> [123] "recount_qc.star.number_of_splices:_annotated_(sjdb)2"
#> [124] "recount_qc.star.number_of_splices:_gc/ag"
#> [125] "recount_qc.star.number_of_splices:_gc/ag2"
#> [126] "recount_qc.star.number_of_splices:_gt/ag"
#> [127] "recount_qc.star.number_of_splices:_gt/ag2"
#> [128] "recount_qc.star.number_of_splices:_non-canonical"
#> [129] "recount_qc.star.number_of_splices:_non-canonical2"
#> [130] "recount_qc.star.number_of_splices:_total"
#> [131] "recount_qc.star.number_of_splices:_total2"
#> [132] "recount_qc.star.uniquely_mapped_reads_%"
#> [133] "recount_qc.star.uniquely_mapped_reads_%2"
#> [134] "recount_qc.star.uniquely_mapped_reads_number"
#> [135] "recount_qc.star.uniquely_mapped_reads_number2"
#> [136] "recount_qc.junction_count"
#> [137] "recount_qc.junction_coverage"
#> [138] "recount_qc.junction_avg_coverage"
#> [139] "recount_qc.star.number_of_input_reads_both"
#> [140] "recount_qc.star.all_mapped_reads_both"
#> [141] "recount_qc.star.number_of_chimeric_reads_both"
#> [142] "recount_qc.star.number_of_reads_mapped_to_multiple_loci_both"
#> [143] "recount_qc.star.number_of_reads_mapped_to_too_many_loci_both"
#> [144] "recount_qc.star.number_of_reads_unmapped:_other_both"
#> [145] "recount_qc.star.number_of_reads_unmapped:_too_many_mismatches_both"
#> [146] "recount_qc.star.number_of_reads_unmapped:_too_short_both"
#> [147] "recount_qc.star.uniquely_mapped_reads_number_both"
#> [148] "recount_qc.star.%_mapped_reads_both"
#> [149] "recount_qc.star.%_chimeric_reads_both"
#> [150] "recount_qc.star.%_reads_mapped_to_multiple_loci_both"
#> [151] "recount_qc.star.%_reads_mapped_to_too_many_loci_both"
#> [152] "recount_qc.star.%_reads_unmapped:_other_both"
#> [153] "recount_qc.star.%_reads_unmapped:_too_many_mismatches_both"
#> [154] "recount_qc.star.%_reads_unmapped:_too_short_both"
#> [155] "recount_qc.star.uniquely_mapped_reads_%_both"
#> [156] "recount_seq_qc.min_len"
#> [157] "recount_seq_qc.max_len"
#> [158] "recount_seq_qc.avg_len"
#> [159] "recount_seq_qc.#distinct_quality_values"
#> [160] "recount_seq_qc.#bases"
#> [161] "recount_seq_qc.%a"
#> [162] "recount_seq_qc.%c"
#> [163] "recount_seq_qc.%g"
#> [164] "recount_seq_qc.%t"
#> [165] "recount_seq_qc.%n"
#> [166] "recount_seq_qc.avgq"
#> [167] "recount_seq_qc.errq"
#> [168] "recount_pred.sample_acc.y"
#> [169] "recount_pred.curated.type"
#> [170] "recount_pred.curated.tissue"
#> [171] "recount_pred.pattern.predict.type"
#> [172] "recount_pred.pred.type"
#> [173] "recount_pred.curated.cell_type"
#> [174] "recount_pred.curated.cell_line"
## Read the metadata files for a project in a collection
## Note: using the test files since I can't access collections right now
## for this collection
ERP110066_collection_meta <- read_metadata(
metadata_files = file_retrieve(
locate_url(
"ERP110066",
"collections/geuvadis_smartseq",
recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3"
)
)
)
#> 2023-05-07 00:12:43.328535 caching file geuvadis_smartseq.recount_project.gz.
#> 2023-05-07 00:12:43.531988 caching file sra.sra.ERP110066.MD.gz.
#> 2023-05-07 00:12:43.724762 caching file sra.recount_project.ERP110066.MD.gz.
#> 2023-05-07 00:12:43.920917 caching file sra.recount_qc.ERP110066.MD.gz.
#> Warning: The 'url' <http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.recount_seq_qc.ERP110066.MD.gz> does not exist or is not available.
#> 2023-05-07 00:12:44.247336 caching file sra.recount_pred.ERP110066.MD.gz.
#> 2023-05-07 00:12:44.448955 caching file geuvadis_smartseq.custom.gz.
dim(ERP110066_collection_meta)
#> [1] 1 161
## New columns for this collection
colnames(ERP110066_collection_meta)[!colnames(ERP110066_collection_meta) %in% colnames(ERP110066_meta)]
#> [1] "custom.sequencing_type"
## Read the metadata for a mouse project
DRP002367_meta <- read_metadata(
metadata_files = file_retrieve(
locate_url("DRP002367", "data_sources/sra", organism = "mouse")
)
)
#> 2023-05-07 00:12:45.597233 caching file sra.sra.DRP002367.MD.gz.
#> 2023-05-07 00:12:46.163738 caching file sra.recount_project.DRP002367.MD.gz.
#> 2023-05-07 00:12:46.506557 caching file sra.recount_qc.DRP002367.MD.gz.
#> 2023-05-07 00:12:47.069095 caching file sra.recount_seq_qc.DRP002367.MD.gz.
#> 2023-05-07 00:12:47.62098 caching file sra.recount_pred.DRP002367.MD.gz.
dim(DRP002367_meta)
#> [1] 4 176
## Locate and read the GTEx bladder metadata
gtex_bladder_meta <- read_metadata(
file_retrieve(
locate_url("BLADDER", "data_sources/gtex")
)
)
#> 2023-05-07 00:12:48.21889 caching file gtex.gtex.BLADDER.MD.gz.
#> 2023-05-07 00:12:48.850269 caching file gtex.recount_project.BLADDER.MD.gz.
#> 2023-05-07 00:12:49.43457 caching file gtex.recount_qc.BLADDER.MD.gz.
#> 2023-05-07 00:12:50.005816 caching file gtex.recount_seq_qc.BLADDER.MD.gz.
dim(gtex_bladder_meta)
#> [1] 21 197
colnames(gtex_bladder_meta)
#> [1] "rail_id"
#> [2] "external_id"
#> [3] "study"
#> [4] "gtex.run_acc"
#> [5] "gtex.subjid"
#> [6] "gtex.sex"
#> [7] "gtex.age"
#> [8] "gtex.dthhrdy"
#> [9] "gtex.sampid"
#> [10] "gtex.smatsscr"
#> [11] "gtex.smcenter"
#> [12] "gtex.smpthnts"
#> [13] "gtex.smrin"
#> [14] "gtex.smts"
#> [15] "gtex.smtsd"
#> [16] "gtex.smubrid"
#> [17] "gtex.smtsisch"
#> [18] "gtex.smtspax"
#> [19] "gtex.smnabtch"
#> [20] "gtex.smnabtcht"
#> [21] "gtex.smnabtchd"
#> [22] "gtex.smgebtch"
#> [23] "gtex.smgebtchd"
#> [24] "gtex.smgebtcht"
#> [25] "gtex.smafrze"
#> [26] "gtex.smgtc"
#> [27] "gtex.sme2mprt"
#> [28] "gtex.smchmprs"
#> [29] "gtex.smntrart"
#> [30] "gtex.smnumgps"
#> [31] "gtex.smmaprt"
#> [32] "gtex.smexncrt"
#> [33] "gtex.sm550nrm"
#> [34] "gtex.smgnsdtc"
#> [35] "gtex.smunmprt"
#> [36] "gtex.sm350nrm"
#> [37] "gtex.smrdlgth"
#> [38] "gtex.smmncpb"
#> [39] "gtex.sme1mmrt"
#> [40] "gtex.smsflgth"
#> [41] "gtex.smestlbs"
#> [42] "gtex.smmppd"
#> [43] "gtex.smnterrt"
#> [44] "gtex.smrrnanm"
#> [45] "gtex.smrdttl"
#> [46] "gtex.smvqcfl"
#> [47] "gtex.smmncv"
#> [48] "gtex.smtrscpt"
#> [49] "gtex.smmppdpr"
#> [50] "gtex.smcglgth"
#> [51] "gtex.smgappct"
#> [52] "gtex.smunpdrd"
#> [53] "gtex.smntrnrt"
#> [54] "gtex.smmpunrt"
#> [55] "gtex.smexpeff"
#> [56] "gtex.smmppdun"
#> [57] "gtex.sme2mmrt"
#> [58] "gtex.sme2anti"
#> [59] "gtex.smaltalg"
#> [60] "gtex.sme2snse"
#> [61] "gtex.smmflgth"
#> [62] "gtex.sme1anti"
#> [63] "gtex.smspltrd"
#> [64] "gtex.smbsmmrt"
#> [65] "gtex.sme1snse"
#> [66] "gtex.sme1pcts"
#> [67] "gtex.smrrnart"
#> [68] "gtex.sme1mprt"
#> [69] "gtex.smnum5cd"
#> [70] "gtex.smdpmprt"
#> [71] "gtex.sme2pcts"
#> [72] "recount_project.project"
#> [73] "recount_project.organism"
#> [74] "recount_project.file_source"
#> [75] "recount_project.metadata_source"
#> [76] "recount_project.date_processed"
#> [77] "recount_qc.aligned_reads%.chrm"
#> [78] "recount_qc.aligned_reads%.chrx"
#> [79] "recount_qc.aligned_reads%.chry"
#> [80] "recount_qc.bc_auc.all_reads_all_bases"
#> [81] "recount_qc.bc_auc.all_reads_annotated_bases"
#> [82] "recount_qc.bc_auc.unique_reads_all_bases"
#> [83] "recount_qc.bc_auc.unique_reads_annotated_bases"
#> [84] "recount_qc.bc_auc.all_%"
#> [85] "recount_qc.bc_auc.unique_%"
#> [86] "recount_qc.bc_frag.count"
#> [87] "recount_qc.bc_frag.kallisto_count"
#> [88] "recount_qc.bc_frag.kallisto_mean_length"
#> [89] "recount_qc.bc_frag.mean_length"
#> [90] "recount_qc.bc_frag.mode_length"
#> [91] "recount_qc.bc_frag.mode_length_count"
#> [92] "recount_qc.exon_fc.all_%"
#> [93] "recount_qc.exon_fc.unique_%"
#> [94] "recount_qc.exon_fc_count_all.total"
#> [95] "recount_qc.exon_fc_count_all.assigned"
#> [96] "recount_qc.exon_fc_count_unique.total"
#> [97] "recount_qc.exon_fc_count_unique.assigned"
#> [98] "recount_qc.gene_fc.all_%"
#> [99] "recount_qc.gene_fc.unique_%"
#> [100] "recount_qc.gene_fc_count_all.total"
#> [101] "recount_qc.gene_fc_count_all.assigned"
#> [102] "recount_qc.gene_fc_count_unique.total"
#> [103] "recount_qc.gene_fc_count_unique.assigned"
#> [104] "recount_qc.intron_sum"
#> [105] "recount_qc.intron_sum_%"
#> [106] "recount_qc.star.%_of_chimeric_reads"
#> [107] "recount_qc.star.%_of_chimeric_reads2"
#> [108] "recount_qc.star.%_of_reads_mapped_to_multiple_loci"
#> [109] "recount_qc.star.%_of_reads_mapped_to_multiple_loci2"
#> [110] "recount_qc.star.%_of_reads_mapped_to_too_many_loci"
#> [111] "recount_qc.star.%_of_reads_mapped_to_too_many_loci2"
#> [112] "recount_qc.star.%_of_reads_unmapped:_other"
#> [113] "recount_qc.star.%_of_reads_unmapped:_other2"
#> [114] "recount_qc.star.%_of_reads_unmapped:_too_many_mismatches"
#> [115] "recount_qc.star.%_of_reads_unmapped:_too_many_mismatches2"
#> [116] "recount_qc.star.%_of_reads_unmapped:_too_short"
#> [117] "recount_qc.star.%_of_reads_unmapped:_too_short2"
#> [118] "recount_qc.star.all_mapped_reads"
#> [119] "recount_qc.star.all_mapped_reads2"
#> [120] "recount_qc.star.average_input_read_length"
#> [121] "recount_qc.star.average_input_read_length2"
#> [122] "recount_qc.star.average_mapped_length"
#> [123] "recount_qc.star.average_mapped_length2"
#> [124] "recount_qc.star.deletion_average_length"
#> [125] "recount_qc.star.deletion_average_length2"
#> [126] "recount_qc.star.deletion_rate_per_base"
#> [127] "recount_qc.star.deletion_rate_per_base2"
#> [128] "recount_qc.star.insertion_average_length"
#> [129] "recount_qc.star.insertion_average_length2"
#> [130] "recount_qc.star.insertion_rate_per_base"
#> [131] "recount_qc.star.insertion_rate_per_base2"
#> [132] "recount_qc.star.mapping_speed,_million_of_reads_per_hour"
#> [133] "recount_qc.star.mapping_speed,_million_of_reads_per_hour2"
#> [134] "recount_qc.star.mismatch_rate_per_base,_%"
#> [135] "recount_qc.star.mismatch_rate_per_base,_%2"
#> [136] "recount_qc.star.number_of_chimeric_reads"
#> [137] "recount_qc.star.number_of_chimeric_reads2"
#> [138] "recount_qc.star.number_of_input_reads"
#> [139] "recount_qc.star.number_of_input_reads2"
#> [140] "recount_qc.star.number_of_reads_mapped_to_multiple_loci"
#> [141] "recount_qc.star.number_of_reads_mapped_to_multiple_loci2"
#> [142] "recount_qc.star.number_of_reads_mapped_to_too_many_loci"
#> [143] "recount_qc.star.number_of_reads_mapped_to_too_many_loci2"
#> [144] "recount_qc.star.number_of_reads_unmapped:_other"
#> [145] "recount_qc.star.number_of_reads_unmapped:_other2"
#> [146] "recount_qc.star.number_of_reads_unmapped:_too_many_mismatches"
#> [147] "recount_qc.star.number_of_reads_unmapped:_too_many_mismatches2"
#> [148] "recount_qc.star.number_of_reads_unmapped:_too_short"
#> [149] "recount_qc.star.number_of_reads_unmapped:_too_short2"
#> [150] "recount_qc.star.number_of_splices:_at/ac"
#> [151] "recount_qc.star.number_of_splices:_at/ac2"
#> [152] "recount_qc.star.number_of_splices:_annotated_(sjdb)"
#> [153] "recount_qc.star.number_of_splices:_annotated_(sjdb)2"
#> [154] "recount_qc.star.number_of_splices:_gc/ag"
#> [155] "recount_qc.star.number_of_splices:_gc/ag2"
#> [156] "recount_qc.star.number_of_splices:_gt/ag"
#> [157] "recount_qc.star.number_of_splices:_gt/ag2"
#> [158] "recount_qc.star.number_of_splices:_non-canonical"
#> [159] "recount_qc.star.number_of_splices:_non-canonical2"
#> [160] "recount_qc.star.number_of_splices:_total"
#> [161] "recount_qc.star.number_of_splices:_total2"
#> [162] "recount_qc.star.uniquely_mapped_reads_%"
#> [163] "recount_qc.star.uniquely_mapped_reads_%2"
#> [164] "recount_qc.star.uniquely_mapped_reads_number"
#> [165] "recount_qc.star.uniquely_mapped_reads_number2"
#> [166] "recount_qc.junction_count"
#> [167] "recount_qc.junction_coverage"
#> [168] "recount_qc.junction_avg_coverage"
#> [169] "recount_qc.star.number_of_input_reads_both"
#> [170] "recount_qc.star.all_mapped_reads_both"
#> [171] "recount_qc.star.number_of_chimeric_reads_both"
#> [172] "recount_qc.star.number_of_reads_mapped_to_multiple_loci_both"
#> [173] "recount_qc.star.number_of_reads_mapped_to_too_many_loci_both"
#> [174] "recount_qc.star.number_of_reads_unmapped:_other_both"
#> [175] "recount_qc.star.number_of_reads_unmapped:_too_many_mismatches_both"
#> [176] "recount_qc.star.number_of_reads_unmapped:_too_short_both"
#> [177] "recount_qc.star.uniquely_mapped_reads_number_both"
#> [178] "recount_qc.star.%_mapped_reads_both"
#> [179] "recount_qc.star.%_chimeric_reads_both"
#> [180] "recount_qc.star.%_reads_mapped_to_multiple_loci_both"
#> [181] "recount_qc.star.%_reads_mapped_to_too_many_loci_both"
#> [182] "recount_qc.star.%_reads_unmapped:_other_both"
#> [183] "recount_qc.star.%_reads_unmapped:_too_many_mismatches_both"
#> [184] "recount_qc.star.%_reads_unmapped:_too_short_both"
#> [185] "recount_qc.star.uniquely_mapped_reads_%_both"
#> [186] "recount_seq_qc.min_len"
#> [187] "recount_seq_qc.max_len"
#> [188] "recount_seq_qc.avg_len"
#> [189] "recount_seq_qc.#distinct_quality_values"
#> [190] "recount_seq_qc.#bases"
#> [191] "recount_seq_qc.%a"
#> [192] "recount_seq_qc.%c"
#> [193] "recount_seq_qc.%g"
#> [194] "recount_seq_qc.%t"
#> [195] "recount_seq_qc.%n"
#> [196] "recount_seq_qc.avgq"
#> [197] "recount_seq_qc.errq"