Kun:LabNotes/SingleCellExpr/2014-6-5: Difference between revisions
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../scripts/get_excluded_sample_id.pl 20131219_C1_hNuc-20140222_mappnig_stats_name_corrected.txt 20140123_C1_hNuc-20140210_mappnig_stats_name_corrected.txt 20140205_C1_hNuc-20140222_mapping_stats_name_corrected.txt 20140212_C1_hNuc-20140222_mapping_stats_name_corrected.txt 20140212_C1_hNuc-20140222_mapping_stats.txt 20140213_C1_hNuc-20140222_mapping_stats_name_corrected.txt 20140218_C1_mapping_stat.txt 20140220_C1_mapping_stat.txt 20140225_C1_mapping_stat.txt 20140226_C1_mapping_stat.txt 20140227_C1_hNuc_mapping_stats.txt 20140311_C1_hNuc_mapping_stats.txt 20140313_C1_hNuc_mapping_stats.txt 20140317_C1_hNuc_mapping_stats.txt 20140304_C1_mapping_stat.txt 20140318_C1_mapping_stat.txt 20140320_C1_mapping_stat.txt 20140321_C1_mapping_stat.txt > 2014_1st_Quater_18_expr_matrix_1N_excluded_ids.txt | ../scripts/get_excluded_sample_id.pl 20131219_C1_hNuc-20140222_mappnig_stats_name_corrected.txt 20140123_C1_hNuc-20140210_mappnig_stats_name_corrected.txt 20140205_C1_hNuc-20140222_mapping_stats_name_corrected.txt 20140212_C1_hNuc-20140222_mapping_stats_name_corrected.txt 20140212_C1_hNuc-20140222_mapping_stats.txt 20140213_C1_hNuc-20140222_mapping_stats_name_corrected.txt 20140218_C1_mapping_stat.txt 20140220_C1_mapping_stat.txt 20140225_C1_mapping_stat.txt 20140226_C1_mapping_stat.txt 20140227_C1_hNuc_mapping_stats.txt 20140311_C1_hNuc_mapping_stats.txt 20140313_C1_hNuc_mapping_stats.txt 20140317_C1_hNuc_mapping_stats.txt 20140304_C1_mapping_stat.txt 20140318_C1_mapping_stat.txt 20140320_C1_mapping_stat.txt 20140321_C1_mapping_stat.txt > 2014_1st_Quater_18_expr_matrix_1N_excluded_ids.txt | ||
../scripts/filterExprMatrix.pl 2014_1st_Quater_18_expr_matrix.txt ../summary_stats/2014_1st_Quater_18_expr_matrix_1N_excluded_ids.txt > 2014_1st_Quater_18_1N_expr_matrix_filtered.txt | ../scripts/filterExprMatrix.pl 2014_1st_Quater_18_expr_matrix.txt ../summary_stats/2014_1st_Quater_18_expr_matrix_1N_excluded_ids.txt > 2014_1st_Quater_18_1N_expr_matrix_filtered.txt | ||
A total of 728 data sets (10323 genes) were obtained after the filtering (at least 1M total reads; mapping rate >0.4; # ERCC detected > 24; % ERCC reads < 0.3; <30% missing values per gene). |
Revision as of 06:25, 6 June 2014
Preparing the 2014Jun data set
Data source
- The data came from 18 C1 experiments.
- 20131219_C1_hNuc-20140222_Expt123Hiseq(oligo dT only)
- 20140123_C1_hNuc-20140210_Expt119HiSeq
- 20140205_C1_hNuc-20140222_Expt123Hiseq
- 20140212_C1_hNuc-20140222_Expt123Hiseq
- 20140213_C1_hNuc-20140222_Expt123Hiseq
- 20140218_C1_hNuc-20140317_Expt128HiSeq
- 20140220_C1_hNuc-20140317_Expt128HiSeq
- 20140225_C1_hNuc-20140317_Expt128HiSeq
- 20140226_C1_hNuc-20140317_Expt128HiSeq
- 20140227_C1_hNuc-20140414_Expt131HiSeq
- 20140313_C1_hNuc-20140414_Expt131HiSeq
- 20140317_C1_hNuc-20140414_Expt131HiSeq
- 20140304_C1_hNuc-20140521_Expt138HiSeq
- 20140318_C1_hNuc-20140521_Expt138HiSeq
- 20140320_C1_hNuc-20140521_Expt138HiSeq
- 20140321_C1_hNuc-20140521_Expt138HiSeq
cd /home/kunzhang/RNAseq/SCAP/expr_matrix ../scripts/merge_expr_matrix.pl 20131219_C1_hNuc-20140222_TPM_matrix_name_corrected.txt 20140210_96Samples_hNuc_Expt119HiSeq_C1_STAR_0123_TPM_matrix_name_corrected.txt 20140205_C1_hNuc-20140222_TPM_matrix_name_corrected.txt 20140212_C1_hNuc-20140222_TPM_matrix_name_corrected.txt 20140213_C1_hNuc-20140222_TPM_matrix_name_corrected.txt 20140218_C1_hNuc_expr_matrix.txt 20140220_C1_hNuc_expr_matrix.txt 20140225_C1_hNuc_expr_matrix.txt 20140226_C1_hNuc_expr_matrix.txt 20140227_C1_hNuc_expr_matrix.txt 20140311_C1_hNuc_expr_matrix.txt 20140313_C1_hNuc_expr_matrix.txt 20140317_C1_hNuc_expr_matrix.txt 20140304_C1_hNuc_expr_matrix.txt 20140318_C1_hNuc_expr_matrix.txt 20140320_C1_hNuc_expr_matrix.txt 20140321_C1_hNuc_expr_matrix.txt > 2014_1st_Quater_18_expr_matrix.txt cd ../summary_stats ../scripts/get_excluded_sample_id.pl 20131219_C1_hNuc-20140222_mappnig_stats_name_corrected.txt 20140123_C1_hNuc-20140210_mappnig_stats_name_corrected.txt 20140205_C1_hNuc-20140222_mapping_stats_name_corrected.txt 20140212_C1_hNuc-20140222_mapping_stats_name_corrected.txt 20140212_C1_hNuc-20140222_mapping_stats.txt 20140213_C1_hNuc-20140222_mapping_stats_name_corrected.txt 20140218_C1_mapping_stat.txt 20140220_C1_mapping_stat.txt 20140225_C1_mapping_stat.txt 20140226_C1_mapping_stat.txt 20140227_C1_hNuc_mapping_stats.txt 20140311_C1_hNuc_mapping_stats.txt 20140313_C1_hNuc_mapping_stats.txt 20140317_C1_hNuc_mapping_stats.txt 20140304_C1_mapping_stat.txt 20140318_C1_mapping_stat.txt 20140320_C1_mapping_stat.txt 20140321_C1_mapping_stat.txt > 2014_1st_Quater_18_expr_matrix_1N_excluded_ids.txt ../scripts/filterExprMatrix.pl 2014_1st_Quater_18_expr_matrix.txt ../summary_stats/2014_1st_Quater_18_expr_matrix_1N_excluded_ids.txt > 2014_1st_Quater_18_1N_expr_matrix_filtered.txt
A total of 728 data sets (10323 genes) were obtained after the filtering (at least 1M total reads; mapping rate >0.4; # ERCC detected > 24; % ERCC reads < 0.3; <30% missing values per gene).