Open biochristmas opened 1 month ago
The TotalEvents
columns in the summary file are the total number of events in the MATS output files: https://github.com/Xinglab/rmats-turbo/issues/257#issuecomment-1419471666
Since you only have --b1
without --b2
the events are not filtered and could be from the --gtf
without supporting reads: https://groups.google.com/g/rmats-user-group/c/SVlOJs4CwVk/m/IIzvDAXrBgAJ
You could get an AS event count by filtering on the read count (IJC_SAMPLE_1, SJC_SAMPLE_1) and PSI (IncLevel1) columns: https://github.com/Xinglab/rmats-turbo/issues/183#issuecomment-1054318031
Hi, @EricKutschera I will filter based on Average PSI (IncLevel) within 0.05 and 0.95. I have three replicates, as an example (first row of the image), Average PSI (IncLevel) = (NA+1.0+0.0)/3. However, there are NA values present. How should I handle this。
You can try different methods for handling NA. One option is to filter out events that have any NA value in IncLevel1. It looks like only a few rows in the screenshot have NA IncLevel1. You could also keep events with only 1 NA value in IncLevel1 and average the remaining values. In the example you mentioned you could use (1 + 0)/2=0.5
as the average PSI
Hi, @EricKutschera
I have another question. IncLevel1 = SJC_SAMPLE_1 / (SJC_SAMPLE_1 + IJC_SAMPLE_2). For example, in the second row of the image, the value for the third replicate should be 0.06: 2/(2+31)=0.06. However, IncLevel1 = 0.037.
IncLevel1 is (IJC_SAMPLE_1/IncFormLen) / ((IJC_SAMPLE_1/IncFormLen) + (SJC_SAMPLE_1/SkipFormLen))
: https://github.com/Xinglab/rmats-turbo/issues/349
Your screenshot doesn't show the IncFormLen and SkipFormLen columns for that event, but based on the coordinates and --readLength 150
they should be 252 and 149. Then IncLevel=(2/252)/((2/252)+(31/149)) = 0.0367
@EricKutschera Thank you for your prompt response. The issue has been resolved. Best regards and good luck!
Yes rMATS can detect events just from the GTF file. See this comment which has a link to an empty bam file: https://github.com/Xinglab/rmats-turbo/issues/79#issuecomment-764704152
You could find the set of annotated events by running rmats with a GTF file and with a mostly empty input
Based on the screenshot I think rMATS will only detect 2 RI events. See this post for details about the intron detection code: https://github.com/Xinglab/rmats-turbo/issues/17
Hi, If I only need to obtain the AS count for a single sample (experimental group or control group), I execute this command: rmats.py --b1 b2.txt --gtf isoquant_gffcompare.gtf -t paired --bi ./STAR_binary_index --readLength 150 --nthread 30 --od ./test1 --libType fr-unstranded --statoff --tmp ./test1/tmp_output. The AS count in the resulting summary.txt file represents the number of alternative splicing events for that sample?![summary](https://github.com/user-attachments/assets/21d4a3c1-71ec-4ce1-b93d-ab3a68c263ca)