I'm using MISO (v 0.4.9) to look at changes in isoform usage in some mouse RNA-seq data. I need to parse out the number of reads assigned to each isoform for each gene (the "assigned_counts" column in the summary output file).
For some transcripts, the number of isoforms that are assigned a PSI value is not the same as the number of transcripts that are assigned read counts. Does anyone know the reason for this?
An example line is below:
In this case, there are seven isoforms with PSI values but only six with assigned reads.
The genes that have this are not consistent between samples. For example, the gene above exhibits this behaviour in the miso summary file for one sample but not in another. All analyses were performed using the same GFF file.
Thanks!
Mike
For some transcripts, the number of isoforms that are assigned a PSI value is not the same as the number of transcripts that are assigned read counts. Does anyone know the reason for this?
An example line is below:
Code:
ENSMUSG00000024993 0.00,0.00,0.00,0.09,0.01,0.88,0.01 0.00,0.00,0.00,0.01,0.00,0.68,0.00 0.02,0.01,0.01,0.29,0.03,0.97,0.02 'exon:ENSMUST00000148577:1_exon:ENSMUST00000148577:2_exon:ENSMUST00000148577:3_exon:ENSMUST00000148577:4','exon:ENSMUST00000142375:1_exon:ENSMUST00000142375:2_exon:ENSMUST00000142375:3','exon:ENSMUST00000136146:1_exon:ENSMUST00000136146:2','exon:ENSMUST00000025957:1_exon:ENSMUST00000025957:2_exon:ENSMUST00000025957:3_exon:ENSMUST00000025957:4_exon:ENSMUST00000025957:5_exon:ENSMUST00000025957:6_exon:ENSMUST00000025957:7_exon:ENSMUST00000025957:8_exon:ENSMUST00000025957:9','exon:ENSMUST00000147049:1_exon:ENSMUST00000147049:2','exon:ENSMUST00000119633:1_exon:ENSMUST00000119633:2_exon:ENSMUST00000119633:3_exon:ENSMUST00000119633:4_exon:ENSMUST00000119633:5_exon:ENSMUST00000119633:6_exon:ENSMUST00000119633:7_exon:ENSMUST00000119633:8','exon:ENSMUST00000128357:1_exon:ENSMUST00000128357:2_exon:ENSMUST00000128357:3_exon:ENSMUST00000128357:4_exon:ENSMUST00000128357:5_exon:ENSMUST00000128357:6_exon:ENSMUST00000128357:7' (0,0,0,0,0,0,0):1,(0,0,0,0,1,0,0):3,(0,0,0,0,1,1,1):4,(0,0,0,1,0,1,0):266,(0,0,0,1,0,1,1):18,(0,1,0,1,0,1,0):10,(0,1,0,1,0,1,1):1,(1,0,0,1,0,1,1):5,(1,0,0,1,1,1,1):4,(1,0,1,1,1,1,1):10 0:0,1:0,2:1,3:26,4:3,5:291 19 + 60811611,60830552,60812040,60811611,60811596,60811591,60811585 60822406,60835113,60814761,60836227,60818439,60836227,60830864
The genes that have this are not consistent between samples. For example, the gene above exhibits this behaviour in the miso summary file for one sample but not in another. All analyses were performed using the same GFF file.
Thanks!
Mike
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