Jome0169
commented
4 years ago 5/19/2020
Generating metaplots of genes which are on and off
Genes which are on are those >1 tpm and are mappable for each of the tissue types - the list I'm working on for this set of files if found here - /scratch/jpm73279/04.lncRNA/02.Analysis/37.control_proportion_lncRNAs_expressed_captured/02.TPM_passing_mappability and the files are named RNA_B73_ear_TPM.surviving.txt RNA_B73_leaf_TPM.surviving.txt RNA_B73_root_TPM.surviving.txt
Script to generate on/off files
1 set -euxo pipefail
2 awk '$2 < 1 {print $1}' ${1} > ${2}_off_gene_list.txt
3 grep -f ${2}_off_gene_list.txt mappable_genes.values.passing.bed > ${2}_off_genes.bed
4
5 awk '$2 >= 1 {print $1}' ${1} > ${2}_on_gene_list.txt
6 grep -f ${2}_on_gene_list.txt mappable_genes.values.passing.bed > ${2}_on_genes.bed Run using the command: parallel 'bash generate_on_off_genes.sh {} {.}' ::: *.txt
Selected Alternative Species
Not all species are of equal quality, since this analysis is dependent on the quality of ChIP-seq data, I'm biasing the further analysis to genomes with good ChIP data. The species to be used are
- S. Virdis
- G. max
- Asparagus
- Sorghum Bicolor
- Phaseolus vulgaris
- Brachypodium d
Here we're finding 15,456 peaks of Elongation overlapping each other, but the upset we're only capturing 8,000 regions, opening up the question - wtf is happening to those other ~8000 peaks
Ear K36me3
Leaf K4me1
Leaf K36me3
Ear K4me1
Leaf K56ac (just curious)
Leaf K36me3
(42.5 Kb)
5/12/2019
Alternative Species
Downloaded the other species data in the directory
/scratch/jpm73279/04.lncRNA/06.annotate_other_species_2020-05-11using the scriptsubmit_fastq_dump_download.sh. I have now downloaded all the species Zefu has given me which is excellent. Now, I just need to modify the pipeline in such as way as to more pliable in regards to the inclusion of having replicates or not.Getting the species into the correct formats I think will be a little irritating, as they are all going to require me to weed out scaffold level assemblies, as well as generate the separate lincRNA files for each genome. Initially I think I should start on maybe getting the most interesting genomes going first - focusing on sorghum, Asparagus, Eutreme, Gycine Max
Final Metaplots
I've generated what feels like maybe 1000 metaplots, but I like to think we're closing in on the final set of metaplots.
5/15/2019
Alternative Species Continuted
Generated the directory structure for alternative species, which looks like this: ├── 05.A_officialnalis │ ├── 00.data │ │ ├── bed_file │ │ ├── chip_seq │ │ │ ├── H3 │ │ │ ├── H3K27me3 │ │ │ ├── H3K36me3 │ │ │ ├── H3K4me1 │ │ │ ├── H3K4me3 │ │ │ ├── H3K56ac │ │ │ ├── H3K9 │ │ │ └── input │ │ ├── reference │ │ └── rna
Based off of the structure which I used for Z.mays. Probably overkill, but this is what is going to allow me to quickly implement this in other species