MaizeSatelliteEvolution

Repeat Consensus Sequences : https://github.com/dawelab/ETR_in_HiFi/tree/main/Consensus_Repeats

outputs: https://github.com/dawelab/MaizeSatelliteEvolution/tree/main/out

figures: https://github.com/dawelab/MaizeSatelliteEvolution/tree/main/figures

Project outline:

1. Issues in OLD Assemblies Repeat Content Estimation.

   • Repeats in Raw Data, mapping : Long reads from Gapless Ab10 assemly are aligned to the gapless Ab10 assembly using minimap2. Read hits are filtered to a single positions (2308) and averaged in 10kb windows. https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/OldAssem_ReadsAlign_RepContent.sh

2. Issues in NEW Assemblies

   Repeat Content Estimation.

   • HiFi Reads Prep : Raw HiFi are converted to CCS in 10 chunks, then bam files are merged together, filtered to a minimum quality of 99%, and converted to a fastq. https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/HiFi_reads_DownPrep.sh

   HiFi Assembly and Annotation.

   • HiFi Contig Generation, summary, scaffolding, annotation : Contigs with > 1/2 the expected read depth are extracted and scaffolded on Mo17 T2T and B73v5 as an alternate. Assemblies annotated with Liftoff. Repeat content assessed. https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/HiFiScaffolding.sh

   • CG119 correction: The incorrectly placed contig is moved with bedtools and remerged into a new assembly. https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/CG119_correction.sh

   • HiFi Reads Repeats, Length, Coverage , Quality : CCS reads are compared to repeat consensus sequences using blast. Total repeat content is then calculated.Then, contigs are generated and the same process is repeated. Finally, the contig v satellite repeat output is used to check for anchored ends on contigs, defined as contigs that do not have a satellite hit within 100bp of start or end bp. https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/RepContentAndContigAnchor.sh

   • biases

     flow cell code: https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/flowcell_bias.sh

     length bias : https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/length_bias.sh

3. Arrays Conserved Repeat Positions.

   • Finding Arrays : Repeat hits within 10kb were merged using bedtools. Arrays with >=10 monomers and >= 10% repeat content were defined as repeat arrays. Array positions were then compared to 100N gaps using bedtools. Then, array positions were compared to core genes using bedtools closest. https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/ArrayPositions.sh

   • Conserved Array Positions : Array positions were clustered together based on repeat type and shared up and down core genes. https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/Conserved_Arrays.R

4. Structure

   Repeat Structure.

   • Model : Classification model creation from sample data. LDA model chosen to further analysis. https://github.com/dawelab/MaizeSatelliteEvolution/tree/main/Model_Classification
   • Raw reads : Raw repeat structure predicted from monomer similarity network toplogy using LDA model. https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/Raw_Structure.sh
   • Assembly structure : Assembly reoeat structure predicted using non-overlapping 10kb bins from monomer similarity network toplogy using LDA model. https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/ArrayStructure.sh
   • Assessing HOR structure: labeling monomers by cluster, checking character string for repeating kmers https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/HOR_re-eval.sh

5. Similarity blocks

   • all to all monomers for 1Mb regions https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/SimilarityBlocks.sh

6. Shared HOR patterns

   • Generating consensus monomers for all identified HOR's https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/HOR_reclustering.sh
   • clustering consensus monomers and looking for patterns https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/HOR_recluster_Pattern.sh
   • Purity of shared patterns and pulling HORs that occur multiple times within one array https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/functions/Shared_HOR_purity.R
   • Shared HOR's among all knob180 arrays in CG108 https://github.com/dawelab/MaizeSatelliteEvolution/blob/67073f6893c2d6417749dac8a8b1b46fb7968361/src/SHARED_HORknobs.sh

7. Repeat Array Comparisons

   • Grouping homologous arrays-- dot plots https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/Array_Homolog_Grouping.sh
   • Grouping homologous arrays-- pariwise comparisons https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/Homolog_Similiarity.sh
   • Array dot plot generation and summary in R -- specific information for Mo17 and CG!08 https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/HomologousArrayComps.R

8. Chip-seq

   • Chipseq alignemnt to Mo17, using unique k-mers https://github.com/dawelab/MaizeSatelliteEvolution/blob/main/src/chip_Mo17.sh
   • plotting in R with patterns <<<<< insert code >>>>