RNAseq analysis of microbe experiment run by Marc Brock.
RNA libraries prepared by Amaryllis and sequenced at UCD
Download link: https://slims.bioinformatics.ucdavis.edu/solexa/view_run.php?id=3587
Julin Downloaded fastq files to Barbera /share/malooflab/Fastqs/Brapa_microbe/timecourse-2018/
Download command was:
wget -r -nd http://slimsdata.genomecenter.ucdavis.edu/Data/mx7wuv39pp/Unaligned2/Project_JMMC_WYO004/On the second download reads had not yet been concatenated across multiple lanes. Concatenate with
for f in $(ls *gz | sed s/_L.*// | uniq)
do
echo $f
cat $f* > concatenated/${f}_R1_001.fastq.gz
doneThen delete non-concatenated files and move the concatenated files up a directory level.
See file tube_no_legend_time_course_2018.xlsx
Marc writes:
Here’s an excel file of tube_nos and the associated treatments, time points etc. The only slightly confusing thing is that occasionally a pot assigned to a treatment didn’t have sufficient seedlings etc. and we had to substitute in a backup pot—hence the possible decoupling of pot number and tube number. All that detail being said—the microbial treatments didn’t change—so this shouldn’t change your analysis IMO.
twoafternoon.any.trtlive.samplingday.lrt.DEGs.all _IS NOW twoafternoon.interaction.trtlive.samplingday.lrt.DEGs.all
dge.diurnal34.anytime.DEGs.all IS NOW dge.diurnal34.interaction.trtlive.time.DEGs.all #interaction
dge.diurnal34.trt.DEGs.all IS NOW dge.diurnal34.trtlive.DEGs.all #treatment
dge.diurnal34.trt.DEGs.all IS NOW dge.diurnal34.any.trtlive.DEGs.all # treatment and treatment:time interaction
dge.diurnal1314.anytime.DEGs.all IS NOW dge.diurnal1314.interaction.trtlive.time.DEGs
dge.diurnal1314.trt.DEGs.all IS NOW dge.diurnal1314.trtlive.DEGs.all
dge.diurnal1314.trt.DEGs.all IS NOW dge.diurnal1314.any.trtlive.DEGs.all
library("phyloseq")
phyloseq_object <- readRDS(file="path/to/rhizo.ps")
otu_table(phyloseq_object) # the read count data
tax_table(phyloseq_object) # taxonomy data
sample_data(phyloseq_object) # sample information