Closed huiWyuan closed 6 years ago
Hi,
Would you show me the commands (parameters) you used, how many input samples you have (under which condition) and the sequencing depth of the samples?
Hi Thank you for your reply. My commands are show below(all sample has 2 replicates) bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_A.sh --Folder /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master --JuncThreshold 5 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --IRthreshold 5 --Readlength 76 --Thread 10 --Condition1SampleName c1_rep1,c1_rep2 --Condition2SampleName c2_rep1,c2_rep2
Rscript /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/R_script_JUM.R experiment_design.txt > outputFile.Rout 2> errorFile.Rout
bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_B.sh --Folder /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master --Test pvalue --Cutoff 1 --TotalFileNum 4 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --Condition1SampleName c1_rep1,c1_rep2 --Condition2SampleName c2_rep1,c2_rep2
bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_C.sh --Folder /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/ --Test pvalue --Cutoff 1 --TotalCondition1FileNum 2 --TotalCondition2FileNum 2 --REF /home/lfgu/bigdata/hitseq/xkcui/output_CLIP_seq_PE_STAR/GFFuniq/gmax.gp
OK. I need the following things from you: 1) When you run the JUM scripts, were there any error messages? 2) Can you send me the "ls -l -t" results in the folder temp_JUM_A_run 3) Can you send me the "ls -l -t" results in the folder JUM_diff 4) Can you send me the "ls -l -t" results in the folder temp_JUM_B_run_pvalue_1 5) Can you send me the "ls -l -t" results in the folder temp_JUM_C_run
2)-4) is for me to check the temporary files generated during each JUM scripts.
On Thu, Aug 9, 2018 at 7:19 PM wanghuiyuan notifications@github.com wrote:
Hi Thank you for your reply. My commands are show below(all sample has 2 replicates) bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_A.sh --Folder /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master --JuncThreshold 5 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --IRthreshold 5 --Readlength 76 --Thread 10 --Condition1SampleName c1_rep1,c1_rep2 --Condition2SampleName c2_rep1,c2_rep2
Rscript /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/R_script_JUM.R experiment_design.txt > outputFile.Rout 2> errorFile.Rout
bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_B.sh --Folder /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master --Test pvalue --Cutoff 1 --TotalFileNum 4 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --Condition1SampleName c1_rep1,c1_rep2 --Condition2SampleName c2_rep1,c2_rep2
bash /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/JUM_C.sh --Folder /home/lfgu/bigdata/hitseq/why/bin/tool/JUM-master/ --Test pvalue --Cutoff 1 --TotalCondition1FileNum 2 --TotalCondition2FileNum 2 --REF /home/lfgu/bigdata/hitseq/xkcui/output_CLIP_seq_PE_STAR/GFFuniq/gmax.gp
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Hi Actually, there are no error messages when I run the JUM_A.sh in the first step. But all intersect_short_intron2 files are zero in temp_JUM_A_run. Is that normal? -rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:50 c1_rep1Aligned.out_intersect_short_intron2.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep1Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep1Aligned.out_intersect_short_intron2_count_table -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep1Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:50 c1_rep2Aligned.out_intersect_short_intron2.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep2Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep2Aligned.out_intersect_short_intron2_count_table -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep2Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:52 c2_rep1Aligned.out_intersect_short_intron2.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep1Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep1Aligned.out_intersect_short_intron2_count_table -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep1Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:48 c2_rep2Aligned.out_intersect_short_intron2.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep2Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep2Aligned.out_intersect_short_intron2_count_table -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep2Aligned.out_intersect_short_intron2_edited.txt
there are no error messages when I run the R_script_JUM.R In the second step. All files in JUM_diff are normal -rw-rw-r-- 1 lfgu lfgu 9.8M Aug 10 02:06 AS_differential.txt drwxrwxr-x 3 lfgu lfgu 8.0K Aug 10 02:56 FINAL_JUM_OUTPUT_pvalue_1 -rw-rw-r-- 1 lfgu lfgu 1.5M Aug 9 20:06 UNION_junc_coor_with_junction_ID_more_than_5_read_in_at_least_2_samples.txt -rw-rw-r-- 1 lfgu lfgu 365M Aug 10 00:01 c1_rep1Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep1_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 358M Aug 10 00:01 c1_rep2Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep2_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 430M Aug 10 00:01 c2_rep1Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep1_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 402M Aug 9 23:59 c2_rep2Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep2_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 7.1M Aug 10 00:02 combined_AS_JUM.gff -rw-rw-r-- 1 lfgu lfgu 1.9K Aug 10 02:03 errorFile.Rout -rw-rw-r-- 1 lfgu lfgu 79 Aug 10 01:53 experiment_design.txt -rw-rw-r-- 1 lfgu lfgu 843K Aug 9 20:06 more_than_5_profiled_total_AS_event_junction_first_processing_for_JUM_reference_building.txt -rw-rw-r-- 1 lfgu lfgu 214 Aug 10 02:00 outputFile.Rout drwxrwxr-x 4 lfgu lfgu 12K Aug 10 02:51 temp_JUM_B_run_pvalue_1
when I run the JUM_B.sh In the third step. some files in temp_JUM_B_run_pvalue_1 are abnormal
-rw-rw-r-- 1 lfgu lfgu 6.9M Aug 10 02:47 AS_differential_JUM_output.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_JUM_output_total_MXE.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_JUM_output_total_cassette_exon.txt -rw-rw-r-- 1 lfgu lfgu 1.7M Aug 10 02:51 AS_differential_JUM_output_total_mixed.txt -rw-rw-r-- 1 lfgu lfgu 9.8M Aug 10 02:47 AS_differential_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_A3SS_event_AS_structure_list.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_A5SS_event_AS_structure_list.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_MXE_AS_event_list.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_cassette_exon_AS_event_list.txt -rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_pvalue_1_long_intron_retention_passing_filter_combined_list.txt -rw-rw-r-- 1 lfgu lfgu 64K Aug 10 02:51 AS_differential_pvalue_1_mixed_AS_event_list.txt -rw-rw-r-- 1 lfgu lfgu 190K Aug 10 02:47 AS_differential_pvalue_1_non_intron_retention_AS_structure_list.txt -rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_pvalue_1_valid_long_intron_retention_list.txt -rw-rw-r-- 1 lfgu lfgu 8.2K Aug 10 02:47 AS_differential_pvalue_1_valid_short_intron_retention_list.txt -rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_total_long_intron_retention_passing_filter_combined_list.txt -rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_total_valid_long_intron_retention_list.txt -rw-rw-r-- 1 lfgu lfgu 8.2K Aug 10 02:47 AS_differential_total_valid_short_intron_retention_list.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 MXE_coordinate_sorted.bed -rw-rw-r-- 1 lfgu lfgu 365M Aug 10 02:48 c1_rep1Aligned.out_coverage_sorted.bed -rw-rw-r-- 1 lfgu lfgu 85M Aug 10 02:48 c1_rep1_coverage_temp_long_intron_overlap_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 85M Aug 10 02:49 c1_rep1_coverage_temp_long_intron_overlap_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_coverage_temp_total_MXE_intersect.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_coverage_temp_total_cassette_intersect.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49 c1_rep1_long_intron_retention_screening_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50 c1_rep1_long_intron_retention_screening_total.txt -rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:48 c1_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:50 c1_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_temp_total_MXE_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep1_temp_total_MXE_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_temp_total_cassette_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep1_temp_total_cassette_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:49 c1_rep1_valid_long_intron_retention_event_list_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:50 c1_rep1_valid_long_intron_retention_event_list_total.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep1_valid_total_MXE_event_ID.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep1_valid_total_cassette_exon_event_ID.txt -rw-rw-r-- 1 lfgu lfgu 358M Aug 10 02:48 c1_rep2Aligned.out_coverage_sorted.bed -rw-rw-r-- 1 lfgu lfgu 82M Aug 10 02:48 c1_rep2_coverage_temp_long_intron_overlap_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 82M Aug 10 02:49 c1_rep2_coverage_temp_long_intron_overlap_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_coverage_temp_total_MXE_intersect.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_coverage_temp_total_cassette_intersect.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49 c1_rep2_long_intron_retention_screening_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50 c1_rep2_long_intron_retention_screening_total.txt -rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:48 c1_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:49 c1_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_temp_total_MXE_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep2_temp_total_MXE_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_temp_total_cassette_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep2_temp_total_cassette_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:49 c1_rep2_valid_long_intron_retention_event_list_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:50 c1_rep2_valid_long_intron_retention_event_list_total.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep2_valid_total_MXE_event_ID.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep2_valid_total_cassette_exon_event_ID.txt -rw-rw-r-- 1 lfgu lfgu 430M Aug 10 02:48 c2_rep1Aligned.out_coverage_sorted.bed -rw-rw-r-- 1 lfgu lfgu 115M Aug 10 02:48 c2_rep1_coverage_temp_long_intron_overlap_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 115M Aug 10 02:49 c2_rep1_coverage_temp_long_intron_overlap_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep1_coverage_temp_total_MXE_intersect.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep1_coverage_temp_total_cassette_intersect.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49 c2_rep1_long_intron_retention_screening_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50 c2_rep1_long_intron_retention_screening_total.txt -rw-rw-r-- 1 lfgu lfgu 313M Aug 10 02:48 c2_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 313M Aug 10 02:50 c2_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep1_temp_total_MXE_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c2_rep1_temp_total_MXE_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep1_temp_total_cassette_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c2_rep1_temp_total_cassette_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:49 c2_rep1_valid_long_intron_retention_event_list_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 c2_rep1_valid_long_intron_retention_event_list_total.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c2_rep1_valid_total_MXE_event_ID.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c2_rep1_valid_total_cassette_exon_event_ID.txt -rw-rw-r-- 1 lfgu lfgu 402M Aug 10 02:48 c2_rep2Aligned.out_coverage_sorted.bed -rw-rw-r-- 1 lfgu lfgu 103M Aug 10 02:48 c2_rep2_coverage_temp_long_intron_overlap_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 103M Aug 10 02:49 c2_rep2_coverage_temp_long_intron_overlap_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep2_coverage_temp_total_MXE_intersect.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep2_coverage_temp_total_cassette_intersect.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49 c2_rep2_long_intron_retention_screening_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50 c2_rep2_long_intron_retention_screening_total.txt -rw-rw-r-- 1 lfgu lfgu 313M Aug 10 02:48 c2_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 313M Aug 10 02:49 c2_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep2_temp_total_MXE_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c2_rep2_temp_total_MXE_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c2_rep2_temp_total_cassette_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c2_rep2_temp_total_cassette_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 19K Aug 10 02:49 c2_rep2_valid_long_intron_retention_event_list_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 19K Aug 10 02:50 c2_rep2_valid_long_intron_retention_event_list_total.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c2_rep2_valid_total_MXE_event_ID.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c2_rep2_valid_total_cassette_exon_event_ID.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 cassette_exon_coordinate_sorted.bed drwxrwxr-x 2 lfgu lfgu 4.0K Aug 10 02:50 con1_3 drwxrwxr-x 2 lfgu lfgu 4.0K Aug 10 02:50 con2_3 -rw-rw-r-- 1 lfgu lfgu 2.8M Aug 10 02:47 left_span_long_intron_AS_differential_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 2.8M Aug 10 02:47 left_span_long_intron_AS_differential_total.txt -rw------- 1 lfgu lfgu 24K Aug 10 02:51 nohup.out -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 non_valid_cassette_exon_list.txt -rw-rw-r-- 1 lfgu lfgu 1.5M Aug 10 02:50 reconstruct_splicing_pattern_input_1.txt -rw-rw-r-- 1 lfgu lfgu 670K Aug 10 02:50 reconstruct_splicing_pattern_input_2.txt -rw-rw-r-- 1 lfgu lfgu 2.8M Aug 10 02:47 right_span_long_intron_AS_differential_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 2.8M Aug 10 02:47 right_span_long_intron_AS_differential_total.txt -rw-rw-r-- 1 lfgu lfgu 7.2K Aug 10 02:47 run.sh -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 temp_MXE -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 temp_cassette -rw-rw-r-- 1 lfgu lfgu 1.5M Aug 10 02:51 temp_intron_retention -rw-rw-r-- 1 lfgu lfgu 987K Aug 10 02:51 temp_intron_retention_consistant -rw-rw-r-- 1 lfgu lfgu 2.9M Aug 10 02:47 temp_long_intron_retention_AS_differential_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 64K Aug 10 02:47 temp_long_intron_retention_AS_differential_pvalue_1_list.txt -rw-rw-r-- 1 lfgu lfgu 2.9M Aug 10 02:47 temp_long_intron_retention_AS_differential_total.txt -rw-rw-r-- 1 lfgu lfgu 64K Aug 10 02:47 temp_long_intron_retention_AS_differential_total_list.txt -rw-rw-r-- 1 lfgu lfgu 171K Aug 10 02:47 temp_long_intron_retention_junction_coordinate_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 171K Aug 10 02:47 temp_long_intron_retention_junction_coordinate_pvalue_1_sorted.txt -rw-rw-r-- 1 lfgu lfgu 171K Aug 10 02:47 temp_long_intron_retention_junction_coordinate_total.txt -rw-rw-r-- 1 lfgu lfgu 171K Aug 10 02:47 temp_long_intron_retention_junction_coordinate_total_sorted.txt -rw-rw-r-- 1 lfgu lfgu 1.7M Aug 10 02:51 temp_mixed -rw-rw-r-- 1 lfgu lfgu 343K Aug 10 02:51 test_intron.txt -rw-rw-r-- 1 lfgu lfgu 67K Aug 10 02:51 test_intron_delta_consistant_and_no_inner_junction_list.txt -rw-rw-r-- 1 lfgu lfgu 84K Aug 10 02:51 test_intron_delta_consistant_list.txt -rw-rw-r-- 1 lfgu lfgu 499 Aug 10 02:51 title -rw-rw-r-- 1 lfgu lfgu 35K Aug 10 02:50 total_A3SS_event.txt -rw-rw-r-- 1 lfgu lfgu 58K Aug 10 02:50 total_A5SS_event.txt -rw-rw-r-- 1 lfgu lfgu 35K Aug 10 02:50 total_cassette_exon_event.txt
Thanks!
If all intersect_short_intron2 files are zero from JUM_A.sh that is fine. It just means that there were no super short intron retention events in your sample.
I can help you debug the JUM_B.sh step. 1) Could you dropbox or google drive share with me the JUM_diff folder (without the temp_JUM_B_run_pvalue_1 and FINAL_JUM_OUTPUT_pvalue_1 subdirectories). Basically, I am going to run JUM_B.sh on my end on your files and see why AS events other than IR were empty. You can share your folder with my email at: qingqing_wang@berkeley.edu. 2) Could you send the two files: errorFile.Rout and outputFile.Rout? These will record detailed information about running the Rscript step.
It is probably not something serious. Just need some checking.
On Thu, Aug 9, 2018 at 8:43 PM wanghuiyuan notifications@github.com wrote:
Hi actually, there are no error messages when I run the JUM_A.sh in the first step. But all intersect_short_intron2 files are zero in temp_JUM_A_run. Is that normal? -rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:50 c1_rep1Aligned.out_intersect_short_intron2.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep1Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep1Aligned.out_intersect_short_intron2_count_table -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep1Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:50 c1_rep2Aligned.out_intersect_short_intron2.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep2Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep2Aligned.out_intersect_short_intron2_count_table -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c1_rep2Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:52 c2_rep1Aligned.out_intersect_short_intron2.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep1Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep1Aligned.out_intersect_short_intron2_count_table -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep1Aligned.out_intersect_short_intron2_edited.txt
-rw-rw-r-- 1 lfgu lfgu 0 Aug 9 23:48 c2_rep2Aligned.out_intersect_short_intron2.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep2Aligned.out_intersect_short_intron2_chr_coor.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep2Aligned.out_intersect_short_intron2_count_table -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 00:01 c2_rep2Aligned.out_intersect_short_intron2_edited.txt
All files in JUM_diff are normal -rw-rw-r-- 1 lfgu lfgu 9.8M Aug 10 02:06 AS_differential.txt drwxrwxr-x 3 lfgu lfgu 8.0K Aug 10 02:56 FINAL_JUM_OUTPUT_pvalue_1 -rw-rw-r-- 1 lfgu lfgu 1.5M Aug 9 20:06 UNION_junc_coor_with_junction_ID_more_than_5_read_in_at_least_2_samples.txt -rw-rw-r-- 1 lfgu lfgu 365M Aug 10 00:01 c1_rep1Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep1_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 358M Aug 10 00:01 c1_rep2Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep2_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 430M Aug 10 00:01 c2_rep1Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep1_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 402M Aug 9 23:59 c2_rep2Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep2_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 7.1M Aug 10 00:02 combined_AS_JUM.gff -rw-rw-r-- 1 lfgu lfgu 1.9K Aug 10 02:03 errorFile.Rout -rw-rw-r-- 1 lfgu lfgu 79 Aug 10 01:53 experiment_design.txt -rw-rw-r-- 1 lfgu lfgu 843K Aug 9 20:06 more_than_5_profiled_total_AS_event_junction_first_processing_for_JUM_reference_building.txt -rw-rw-r-- 1 lfgu lfgu 214 Aug 10 02:00 outputFile.Rout drwxrwxr-x 4 lfgu lfgu 12K Aug 10 02:51 temp_JUM_B_run_pvalue_1
there are no error messages when I run the R_script_JUM.R In the second step. All files in JUM_diff are normal -rw-rw-r-- 1 lfgu lfgu 9.8M Aug 10 02:06 AS_differential.txt drwxrwxr-x 3 lfgu lfgu 8.0K Aug 10 02:56 FINAL_JUM_OUTPUT_pvalue_1 -rw-rw-r-- 1 lfgu lfgu 1.5M Aug 9 20:06 UNION_junc_coor_with_junction_ID_more_than_5_read_in_at_least_2_samples.txt -rw-rw-r-- 1 lfgu lfgu 365M Aug 10 00:01 c1_rep1Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep1_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 358M Aug 10 00:01 c1_rep2Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c1_rep2_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 430M Aug 10 00:01 c2_rep1Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep1_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 402M Aug 9 23:59 c2_rep2Aligned.out_coverage.bed -rw-rw-r-- 1 lfgu lfgu 1.3M Aug 10 00:03 c2_rep2_combined_count.txt -rw-rw-r-- 1 lfgu lfgu 7.1M Aug 10 00:02 combined_AS_JUM.gff -rw-rw-r-- 1 lfgu lfgu 1.9K Aug 10 02:03 errorFile.Rout -rw-rw-r-- 1 lfgu lfgu 79 Aug 10 01:53 experiment_design.txt -rw-rw-r-- 1 lfgu lfgu 843K Aug 9 20:06 more_than_5_profiled_total_AS_event_junction_first_processing_for_JUM_reference_building.txt -rw-rw-r-- 1 lfgu lfgu 214 Aug 10 02:00 outputFile.Rout drwxrwxr-x 4 lfgu lfgu 12K Aug 10 02:51 temp_JUM_B_run_pvalue_1
when I run the JUM_B.sh In the third step. some files in temp_JUM_B_run_pvalue_1 are abnormal
-rw-rw-r-- 1 lfgu lfgu 6.9M Aug 10 02:47 AS_differential_JUM_output.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_JUM_output_total_MXE.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_JUM_output_total_cassette_exon.txt -rw-rw-r-- 1 lfgu lfgu 1.7M Aug 10 02:51 AS_differential_JUM_output_total_mixed.txt -rw-rw-r-- 1 lfgu lfgu 9.8M Aug 10 02:47 AS_differential_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_A3SS_event_AS_structure_list.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_A5SS_event_AS_structure_list.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_MXE_AS_event_list.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:51 AS_differential_pvalue_1_cassette_exon_AS_event_list.txt -rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_pvalue_1_long_intron_retention_passing_filter_combined_list.txt -rw-rw-r-- 1 lfgu lfgu 64K Aug 10 02:51 AS_differential_pvalue_1_mixed_AS_event_list.txt -rw-rw-r-- 1 lfgu lfgu 190K Aug 10 02:47 AS_differential_pvalue_1_non_intron_retention_AS_structure_list.txt -rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_pvalue_1_valid_long_intron_retention_list.txt -rw-rw-r-- 1 lfgu lfgu 8.2K Aug 10 02:47 AS_differential_pvalue_1_valid_short_intron_retention_list.txt -rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_total_long_intron_retention_passing_filter_combined_list.txt -rw-rw-r-- 1 lfgu lfgu 20K Aug 10 02:50 AS_differential_total_valid_long_intron_retention_list.txt -rw-rw-r-- 1 lfgu lfgu 8.2K Aug 10 02:47 AS_differential_total_valid_short_intron_retention_list.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 MXE_coordinate_sorted.bed -rw-rw-r-- 1 lfgu lfgu 365M Aug 10 02:48 c1_rep1Aligned.out_coverage_sorted.bed -rw-rw-r-- 1 lfgu lfgu 85M Aug 10 02:48 c1_rep1_coverage_temp_long_intron_overlap_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 85M Aug 10 02:49 c1_rep1_coverage_temp_long_intron_overlap_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_coverage_temp_total_MXE_intersect.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_coverage_temp_total_cassette_intersect.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49 c1_rep1_long_intron_retention_screening_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50 c1_rep1_long_intron_retention_screening_total.txt -rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:48 c1_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:50 c1_rep1_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_temp_total_MXE_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep1_temp_total_MXE_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep1_temp_total_cassette_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep1_temp_total_cassette_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:49 c1_rep1_valid_long_intron_retention_event_list_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:50 c1_rep1_valid_long_intron_retention_event_list_total.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep1_valid_total_MXE_event_ID.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep1_valid_total_cassette_exon_event_ID.txt -rw-rw-r-- 1 lfgu lfgu 358M Aug 10 02:48 c1_rep2Aligned.out_coverage_sorted.bed -rw-rw-r-- 1 lfgu lfgu 82M Aug 10 02:48 c1_rep2_coverage_temp_long_intron_overlap_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 82M Aug 10 02:49 c1_rep2_coverage_temp_long_intron_overlap_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_coverage_temp_total_MXE_intersect.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_coverage_temp_total_cassette_intersect.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:49 c1_rep2_long_intron_retention_screening_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 82K Aug 10 02:50 c1_rep2_long_intron_retention_screening_total.txt -rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:48 c1_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 312M Aug 10 02:49 c1_rep2_temp_long_intron_retention_junction_coordinate_with_read_num_total.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_temp_total_MXE_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep2_temp_total_MXE_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 0 Aug 10 02:50 c1_rep2_temp_total_cassette_coordinate_with_read_num_per_ID.txt -rw-rw-r-- 1 lfgu lfgu 5 Aug 10 02:50 c1_rep2_temp_total_cassette_with_indicator.txt -rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:49 c1_rep2_valid_long_intron_retention_event_list_pvalue_1.txt -rw-rw-r-- 1 lfgu lfgu 18K Aug 10 02:50 c1_rep2_valid_long_intron_retention_event_list_total.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep2_valid_total_MXE_event_ID.txt -rw-rw-r-- 1 lfgu lfgu 1 Aug 10 02:50 c1_rep2_valid_total_cassette_exon_event_ID.txt
Thanks!
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total AS events output just contain intron_retention(1062). All other AS events is 0. such as A3SS A5SS MXE and cassette_exon