Cuffdiff splicing.diff output
Dear all,
I run cufflinks/cuffmege/cuffdiff pipeline on my data. But I have some problem on how to interpret the splicing.diff results.
Here are some of my results:
test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
TSS2038 XLOC_001278 Q91YR5 chr1:164462249-164478706 g1 g2 OK 0 0 0.358701 2.93163e-09 4.59102e-10 1.52192e-06 yes
TSS745 XLOC_000478 NP_001074727 chr1:138362954-138428088 g1 g2 OK 0 0 0.372363 6.93969e-07 1.27085e-07 0.000210643 yes
TSS30120 XLOC_020929 Q80TA1,uc008wvi.1 chr5:30559157-30849030 g1 g2 OK 0 0 0.278089 3.08277e-06 5.95185e-07 0.00049326 yes
I am wondering how can I find out the splice sites from the splicing.diff results. I'd like to check the significant splicing events visually on a genome browser. But The locus provided in splicing.diff seems to be the locus of the gene/transcript, from which I can't locate the position where the splicing event happens.
Also, I am also confused about how to figure out the AS isoforms that are compared by cuffdiff. For example, if a genes has 5 splicing variant and cuffdiff perform a spilcing test on this gene. How could I identify the two isoforms that are compared by cuffdiff ?
Thanks a lot!
I run cufflinks/cuffmege/cuffdiff pipeline on my data. But I have some problem on how to interpret the splicing.diff results.
Here are some of my results:
test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant
TSS2038 XLOC_001278 Q91YR5 chr1:164462249-164478706 g1 g2 OK 0 0 0.358701 2.93163e-09 4.59102e-10 1.52192e-06 yes
TSS745 XLOC_000478 NP_001074727 chr1:138362954-138428088 g1 g2 OK 0 0 0.372363 6.93969e-07 1.27085e-07 0.000210643 yes
TSS30120 XLOC_020929 Q80TA1,uc008wvi.1 chr5:30559157-30849030 g1 g2 OK 0 0 0.278089 3.08277e-06 5.95185e-07 0.00049326 yes
I am wondering how can I find out the splice sites from the splicing.diff results. I'd like to check the significant splicing events visually on a genome browser. But The locus provided in splicing.diff seems to be the locus of the gene/transcript, from which I can't locate the position where the splicing event happens.
Also, I am also confused about how to figure out the AS isoforms that are compared by cuffdiff. For example, if a genes has 5 splicing variant and cuffdiff perform a spilcing test on this gene. How could I identify the two isoforms that are compared by cuffdiff ?
Thanks a lot!