empty output

[유채영학부생]

Hello, I ran rmats and checked the results, but I found that files except fromGTF files have only headers, and the data is empty. Below is the executed code and the result message. How can I resolve this?

gtf: 33.824291944503784

There are 70711 distinct gene ID in the gtf file

There are 277081 distinct transcript ID in the gtf file

There are 44202 one-transcript genes in the gtf file

There are 1791080 exons in the gtf file

There are 28955 one-exon transcripts in the gtf file

There are 26109 one-transcript genes with only one exon in the transcript

Average number of transcripts per gene is 3.918499

Average number of exons per transcript is 6.464103

Average number of exons per transcript excluding one-exon tx is 7.101735

Average number of gene per geneGroup is 9.138120

statistic: 0.030672788619995117

read outcome totals across all BAMs

USED: 149509

NOT_PAIRED: 0

NOT_NH_1: 29482

NOT_EXPECTED_CIGAR: 715

NOT_EXPECTED_READ_LENGTH: 0

NOT_EXPECTED_STRAND: 0

EXON_NOT_MATCHED_TO_ANNOTATION: 9797

JUNCTION_NOT_MATCHED_TO_ANNOTATION: 289

CLIPPED: 0

total: 189792

outcomes by BAM written to: /Users/yoochaeyeong/desktop/output/2024-01-17-14_51_53_817852_read_outcomes_by_bam.txt

novel: 0.18515801429748535

The splicing graph and candidate read have been saved into /Users/yoochaeyeong/desktop/output/2024-01-17-14_51_53_817852_*.rmats

save: 0.11171293258666992

loadsg: 0.0009050369262695312

==========

Done processing each gene from dictionary to compile AS events

Found 62887 exon skipping events

Found 4909 exon MX events

Found 24333 alt SS events

There are 14870 alt 3 SS events and 9463 alt 5 SS events.

Found 11082 RI events

==========

ase: 2.5969560146331787

count: 0.4099431037902832

Processing count files.

Done processing count files.

python3 rmats.py --b1 /Users/yoochaeyeong/desktop/testData/b1.txt --b2 /Users/yoochaeyeong/desktop/testData/b2.txt --gtf /Users/yoochaeyeong/desktop/gencode.v45.chr_patch_hapl_scaff.annotation.gtf -t single --readLength 50 --nthread 4 --od /Users/yoochaeyeong/desktop/output --tmp /Users/yoochaeyeong/desktop/output

[kutsc...@gmail.com]

By default, the main output files are filtered down to splicing events that have supporting reads from the bam files. The filter requires at least 1 read for each sample group (--b1, --b2) and at least 1 read for the inclusion isoform and at least 1 read for the skipping isoform: https://github.com/Xinglab/rmats-turbo/blob/v4.2.0/rmats.py#L336

If run with --statoff then that filter is not applied. If only the fromGTF files have output then rMATS did not find enough supporting reads for any event. You could try running with --statoff to see the read counts for each event. I think the issue is that there are not enough total reads. The output shows:
USED: 149509
total: 189792

Most of the reads were used, but there aren't that many reads to begin with. See this post: https://groups.google.com/g/rmats-user-group/c/hgEOH_b5Pr0

Eric

[seist1104]

Thank you for your assistance. I tried running the command with the --statoff option, but the results are still the same. What should I do?

Here is my executed code.

python3 rmats.py --b1 /Users/yoochaeyeong/desktop/testData/b1.txt --b2 /Users/yoochaeyeong/desktop/testData/b2.txt --gtf /Users/yoochaeyeong/desktop/gencode.v45.chr_patch_hapl_scaff.annotation.gtf -t single --readLength 50 --nthread 4 --od /Users/yoochaeyeong/desktop/output --tmp /Users/yoochaeyeong/desktop/output --statoff

2024년 1월 17일 수요일 오후 10시 51분 1초 UTC+9에 kutsc...@gmail.com님이 작성:

[kutsc...@gmail.com]

With --statoff I think there should be more than just the header lines in the MATS output files. Maybe there was an error message in the --statoff run. It looks like you used the same --od and --tmp as the previous run which can cause an error if you didn't delete the output from the previous run

Eric