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qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
MIT License
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total AS events output just contain intron_retention #16

Closed huiWyuan closed 6 years ago

huiWyuan commented 6 years ago

total AS events output just contain intron_retention(1062). All other AS events is 0. such as A3SS A5SS MXE and cassette_exon

qqwang-berkeley commented 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?

huiWyuan commented 6 years ago

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

qqwang-berkeley commented 6 years ago

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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huiWyuan commented 6 years ago

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!

qqwang-berkeley commented 6 years ago

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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