Although I’d previously generated some feature stats for this genome annotation (see 20191029), we decided we wanted to get some additional info, similar to that of Table 1 in M.Aranda et al 2016. Scientific Reports.
I’d previously created intron and intergenic features, but didn’t do any sort of analysis on them. In order to try to mirror some of what is in the table linked above, we need some stats from the introns file.
So, I generated some relevant stats with the introns file, as well as some other basic stats. Check out the deets in the Jupyter Notebook linked below.
Jupyter Notebook (GitHub):
from Sam’s Notebook https://ift.tt/2CmOx7b
- I updated my DMR analysis by including reads with MAPQ score of >= 20
- Using methylpy pipeline, I
- created allc files
- created filtered bam files for QC
- ran DMRfind to identify within sample DMRs that show methylation at a significantly different level than would be expected by genetic variation alone
- filtered DMRs for those showing >=5x coverage in 3/4 samples per group. I didn’t use this cutoff for the control samples since these each only has two individuals.
Group stats on DMRs
- To determine if there is a significant experimental effect on DMRs I first arcsin(sqrt) transformed the percent methylation data
- BEFORE transformation percent methylation distribution:
- AFTER transformation percent methylation distribution:
- I ran a 1 way ANOVA to test if sea lice infestation had an effect
- 1 way ANOVA results summary table here: DMR_MCmax25_1wayAOV_infest_modelsumm.csv
- 3 DMRs showed a significant infestation effect at 1way ANOVA p-value of < 0.01
- 13 DMRs showed a significant infestation effect at 1way ANOVA p-value of < 0.05
- 24 DMRs showed a significant infestation effect at 1way ANOVA p-value of < 0.1
Heatmap of 24 DMRs that showed a significant infestation effect at 1way ANOVA p-value of < 0.1. Heatmap key:Column color bar in heat maps below: light pink = 16C_26psu, dark pink = 16C_32psu, light green = 8C_26psu, dark green = 8C_32psu, magenta = CTRL_16C_26psu, cyan = CTRL_8C_26psu. heatmap color: Red = more methylation, blue = no methylation, black = no data.
- For the 24 DMRs that showed a significant infestation effect at 1way ANOVA p-value of < 0.1, I ran a two way ANOVA on their percent methylation to see if temperature, salinity, or their interaction showed a significant effect.
- validate 24 DMRs that showed a significant infestation effect at 1way ANOVA p-value of < 0.1 in IGV
- generate ANOVA filtered bed file
- compare to filtered bam files linked above
- find out where in the genome these DMRs are
from shellytrigg https://ift.tt/32maIoP