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AS events of a single sample #418
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The Since you only have You could get an AS event count by filtering on the read count (IJC_SAMPLE_1, SJC_SAMPLE_1) and PSI (IncLevel1) columns: #183 (comment) |
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 |
Hi, @EricKutschera |
IncLevel1 is Your screenshot doesn't show the IncFormLen and SkipFormLen columns for that event, but based on the coordinates and |
@EricKutschera |
Yes rMATS can detect events just from the GTF file. See this comment which has a link to an empty bam file: #79 (comment)
Based on the screenshot I think rMATS will only detect 2 RI events. See this post for details about the intron detection code: #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?
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