This page is under active construction.
Main result files
1. Splice graph and ASMs
result/splice_graph.gtf and result/asm_path.gtf — gtf tracks for the splice graph and alternative ASM paths.
2. Differentially expressed/transcribed regions
result/differential_expression.txt — summary of differential expression level on genes
| chromosome | chromosome name of the differentially expressed gene |
| position_start | start position of the differentially gene |
| position_end | end position of the differentially gene |
| stat_diff_expr(|stat_d_expected-stat_d|) | statistic of differential gene expression, larger value indicates greater difference (statistical difference) |
| fold_change | fold change from group1 to group2 (practical difference) |
| coverage_group1 | estimated gene expression of group1, measured by read coverage |
| coverage_group2 | estimated gene expression of group2, measured by read coverage |
| significant | whether the difference is significant under the specified false discovery rate |
result/differential_transcription.txt — summary of differential transcription on ASMs
| chromosome | chromosome name of the differentially transcribed ASM |
| position_start | start position of the differentially transcribed ASM |
| position_end | end position of the differentially transcribed ASM |
| category | category of the ASM |
| stat_diff_trans(|stat_d_expected-stat_d|) | statistic of differential ASM transcription, larger value indicates greater difference (statistical difference) |
| sqrtJSD | square root of JSD between group1 and group2 (practical difference), larger value indicates great difference |
| coverage_group1 | estimated ASM expression of group1, measured by read coverage |
| coverage_group2 | estimated ASM expression of group2, measured by read coverage |
| significant | whether the difference is significant under the specified false discovery rate |
3. False discovery rate table
FDR_expression_two_group_comparison.txt and FDR_transcription_two_group_comparison.txt
The statistical significance of the differential signals is measured by the difference between the expected and calculated divergence statistic, |stat_d_expected - stat_d|, and a differential signal will be called significant if such difference is larger than some cutoff delta. Therefore, the selection of delta will affect the set of genes/ASMs called significant and will affect the false discovery rate (FDR). To assist your choice of FDR, we shift the value of delta and provide the number of significant genes/ASMs you will have at different levels of delta. You may choose your desired FDR according to this list and give to DiffSplice (need to rerun the differential test step, specified by -x option, to see the updated results).
Result tracks on UCSC genome browser
To view result tracks on UCSC genome browser, please take the following steps:
1. Upload the two gtf tracks generated by DiffSplice (splice_graph.gtf and asm_path.gtf), either through browser or public server. You may also upload the wiggle files or bigwig files of you data if you have generated them from the SAM/BAM files;
2. Select the region of interest from differential_expression.txt for differentially expressed genes or from differential_transcription.txt for differentially transcribed ASMs;
3. Paste in the region to genome browser and it will lead you to the place with differential expression/transcription;
4. If you are checking a place with differential transcription, the location provided in differential_transcription.txt gives the coordinates of the ASM, not including the surrounding exons. You may zoom out to see the surrounding exons and the whole gene.
Below is an example.
Other result files
1. Splice junctions from RNA-seq alignments
| result/stat/splice_all.bed | all splice junctions from the input RNA-seq alignments |
| result/stat/splice_filtered.bed | splice junctions after filtering |