EricKutschera
commented
1 year ago It looks like most of the genes in the --gtf that you used have only 1 exon. It also looks like other genes have very few exons:
There are 26457 distinct gene ID in the gtf file There are 20548 one-transcript genes with only one exon in the transcript Average number of exons per transcript excluding one-exon tx is 2.528836
The SE event definition requires 3 exons and the MXE event definition requires 4. Probably there are very few genes with enough exons in your --gtf to define those events. rmats also requires some evidence for both the inclusion and skipping isoforms to define an event. Even if there are some 3 exon genes in the --gtf, there may not be evidence for both isoforms
Hi! I have some questions about rmats. Why are there no SE events or MXE events in my results?Are these related to the fact that the intron of the research object is only 15 to 17bp?
python ~/miniconda3/envs/rmats_new/bin/rmats.py --b1 B1_C.txt --gtf ~/Blepharisma_sinuosum/stringtie/gffcom_merge.annotated.gtf --bi ~/Blepharisma_sinuosum/star/star_genome_index --od ~/Blepharisma_sinuosum/rMATs/output/number/C --tmp ~/Blepharisma_sinuosum/rMATs/output/number/tmp_C -t paired --readLength 150 --variable-read-length --statoff --cstat 0.0001 --nthread 12 --novelSS --mil 15 &> studout_statoff_C.txt
gtf: 0.727747917175293 There are 26457 distinct gene ID in the gtf file There are 30732 distinct transcript ID in the gtf file There are 23453 one-transcript genes in the gtf file There are 43695 exons in the gtf file There are 22253 one-exon transcripts in the gtf file There are 20548 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 1.161583 Average number of exons per transcript is 1.421808 Average number of exons per transcript excluding one-exon tx is 2.528836 Average number of gene per geneGroup is 49.204829 statistic: 0.0033485889434814453
read outcome totals across all BAMs USED: 105161131 NOT_PAIRED: 34 NOT_NH_1: 7634801 NOT_EXPECTED_CIGAR: 1375618 NOT_EXPECTED_READ_LENGTH: 0 NOT_EXPECTED_STRAND: 0 EXON_NOT_MATCHED_TO_ANNOTATION: 8799321 JUNCTION_NOT_MATCHED_TO_ANNOTATION: 90385 CLIPPED: 6816475 total: 129877765 outcomes by BAM written to: /apps/users/Gaoqi/Blepharisma_sinuosum/rMATs/output/number/tmp_C/2023-04-21-10_32_31_276569_read_outcomes_by_bam.txt
novel: 439.4744784832001 The splicing graph and candidate read have been saved into /apps/users/Gaoqi/Blepharisma_sinuosum/rMATs/output/number/tmp_C/2023-04-21-10_32_31276569*.rmats save: 0.9797332286834717 loadsg: 0.041941165924072266
========== Done processing each gene from dictionary to compile AS events Found 0 exon skipping events Found 0 exon MX events Found 414 alt SS events There are 291 alt 3 SS events and 123 alt 5 SS events. Found 1377 RI events
Could you please help me with this