# Plants

- Auto-generated Table of Content
[ToC]

## 1. ucDunPrim2
Mito and chloro FastK profiles

So-called Chloroplast reads

### Chloroplast


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### Mito reads - more promissing!


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## 2. dhQueRobu3

### Chloroplast-reads Profiles (Oak)
Plotting Oak (dhQueRobu3) Median and all kmer profiles for chloroplast-selected reads

![](https://i.imgur.com/JKMTBV8.png)

### Assembly graph from hifiasm

gbk.HiFiMapped.bam.filtered.assembled.p_ctg.noseq.gfa.png

gbk.HiFiMapped.bam.filtered.assembled.p_ctg.fa
A = 17206588 (32.1%), C = 9585209 (17.9%), G = 9577275 (17.9%), T = 17187789 (32.1%), CpG = 2187430 (4.1%)
sum = 53556861, n = 1300, mean = 41197.5853846154, largest = 109444, smallest = 20353
N50 = 40889, L50 = 543
N60 = 39505, L60 = 677
N70 = 37627, L70 = 816
N80 = 35337, L80 = 963
N90 = 32726, L90 = 1120
N100 = 20353, L100 = 1300


gbk.HiFiMapped.bam.filtered.assembled.a_ctg.noseq.gfa.png

gbk.HiFiMapped.bam.filtered.assembled.a_ctg.fa
A = 4302158 (32.1%), C = 2372562 (17.7%), G = 2379167 (17.8%), T = 4339884 (32.4%), CpG = 450476 (3.4%)
sum = 13393771, n = 411, mean = 32588.2506082725, largest = 85092, smallest = 13029
N50 = 33824, L50 = 169
N60 = 32300, L60 = 210
N70 = 30175, L70 = 252
N80 = 28049, L80 = 299
N90 = 24758, L90 = 349
N100 = 13029, L100 = 411


### Chloroplast profMedian (Oak)


### Mitochondrion (oak)
Assembly graphs

### r_utg.noseq.gfa

Haplotype-resolved raw unitig graph in GFA format (prefix.r_utg.gfa). This graph keeps all haplotype information, including somatic mutations and recurrent sequencing errors.


### p_utg.noseq.gfa

Haplotype-resolved processed unitig graph without small bubbles (prefix.p_utg.gfa). Small bubbles might be caused by somatic mutations or noise in data, which are not the real haplotype information.


### p_ctg.gfa

Primary assembly contig graph (prefix.p_ctg.gfa). This graph collapses different haplotypes.


Profiles


### Mitohifi-plant for reads from 3000-15000

/lustre/scratch116/tol/projects/darwin/data/dicots/Quercus_robur/working/mito-v2/mitohifi-plant-passedMedian300015000

### Common reads between mito and chloro

How come mitohifi has fished in-common reads ?


Chloroplast reference was
LOCUS NC_046388 161172 bp DNA circular PLN 26-MAR-2020
DEFINITION Quercus robur cultivar Fastigiata chloroplast, complete genome.

LOCUS MN199236 412886 bp DNA circular PLN 04-APR-2020
DEFINITION UNVERIFIED: Quercus variabilis mitochondrion sequence.

Both references dont have much in common


Im re-running mitohifi to be sure I fished the reads in the correct way.

Its confirmed, got the same result as above.

What happens if I assemble those 3 pots separately?

Ok, so now I'm running MitoHifi-plants and MBG to the groups of reads above:

- 65807 reads that are fished only by the ref-chloroplast


- 48289 reads that are fished by both, chloro and mito

![](https://i.imgur.com/O5I2zjZ.png)



- 40543 reads that were fished by ref-mito only


Sergey's result

![](https://i.imgur.com/2D7hWbp.png)


### To dos
- [ ] Hic data
- [x] Assembly graph for hifiasm nuclear 
- [ ] MEGAhit
- [ ] Fly (permissive with gluing things together)
- [ ] jumberDB (DBG-like)





## 3. drPotAnse1 
Potentilla_anserina

ProfMedian Mito-reads


ok, from the image above I got reads from 1200 to 2800. Blast a few and they look like choroplasts!


Tetranucs from Claudia. Blue is the first peak above

-[ ] Running mito-plants for reads in the peak 1200-2800

-[ ] Running mito-plants for reads in the peak 4500-6350

-[ ] Running profs for chloro reads

Chloroplast reads

### drPotAnse1 MBG mito 1k


## 4. drFilUlma1

### Chloroplast
Many different contigs annotated. None is the size or circularizes.

/lustre/scratch116/tol/projects/darwin/data/dicots/Filipendula_ulmaria/working/chloro/chloro-plants
Running profMedian

## 5. ucDunPrim2

To dos:

- [ ] profMedian mito 

- [ ] blast mito and chloro
- [ ] make a venn diagram


## 6. Notes 

Papers: 
- https://www.nature.com/articles/s41598-019-41377-w
- https://www.mdpi.com/2223-7747/10/7/1360/htm

## 7. drAilAlti1

### Mito 
MBG -k 1001 -w 250 -a 5 -u 150 

![](https://i.imgur.com/67Pc923.png)

MBG -k 5001 -w 250 -a 5 -u 150

![](https://i.imgur.com/F3MroDN.png)
 
 4 - chloro
 3 - chloro
 2 - chloro
 1 - chloro
 
 ### Chloro
 
 MBG -k 3001 -w 250 -a 5 -u 150
 
 ![](https://i.imgur.com/5anaDc8.png)



## 7. dcPolAvic1 Polygonum_aviculare 

Mito k1001

![](https://i.imgur.com/PpfABI1.png)

k6001

![](https://i.imgur.com/BAE3SYt.png)


- [ ] recombination of plant mito?
- cat mito & chloro and mapp to it
then select better mapping


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## 8. cbRhyLore1
### 8.1 cbRhyLore1 MBG k=1001

![](https://i.imgur.com/SgLi5Bu.png)


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### 8.2 cbRhyLore1 MBG k=5001


![](https://i.imgur.com/zWKtvmg.png)


### 8.4 Chloroplast


Linear (from MBG k=1001)
![](https://i.imgur.com/ww1roHm.png)


Circular (from MBG k=1001)
![](https://i.imgur.com/YpVM7jA.png)



Chloroplast Pacbio reads coverage 
![](https://i.imgur.com/KTrTZ9H.png)




 contigs_stats.tsv: Related mitogenome is 125195 bp long and has 116 genes


| contig_id | frameshifts? | length(bp) | number of genes | 
| -------- | -------- | -------- | -------- 
| final_mitogenome     | No     | 124828     | 104


Mitohifi run: ```/lustre/scratch116/tol/projects/darwin/data/non-vascular-plants/Rhytidiadelphus_loreus/working/mito_chloroplast/mitohifi_chloro ```


### 8.4.1 ChloroplastChloroplast 10x coverage 

![](https://i.imgur.com/szbDWYP.png)


![](https://i.imgur.com/OeXE83b.png)


Flagstats of mapped 10x reads:

2845471 + 0 in total (QC-passed reads + QC-failed reads)
80651 + 0 secondary
0 + 0 supplementary
531228 + 0 duplicates
2845471 + 0 mapped (100.00% : N/A)
2764820 + 0 paired in sequencing
1383339 + 0 read1
1381481 + 0 read2
1391229 + 0 properly paired (50.32% : N/A)
2738426 + 0 with itself and mate mapped
26394 + 0 singletons (0.95% : N/A)
17598 + 0 with mate mapped to a different chr
7079 + 0 with mate mapped to a different chr (mapQ>=5)

### 8.5 Mitochondria

Linear (MBG k=1001)

![](https://i.imgur.com/IWj7V0L.png)


Circular (MBG k=1001)

![](https://i.imgur.com/c5AVP42.png)



mito 10x coverage

![](https://i.imgur.com/EYSO8yi.png)

ND5
complement(71541..72254)
/translation="E*PTPVSASIHAATMVTAGVFMIARCSPLFEYSSTALIVITFVGA
MTSFFAATTGILQNDLKRVIAYSTCSQLGYMIFACGISNYSVSVFHLMNHAFFKALLFL
SAGSVIHAMSDEQDMRKMGGLASLLPFTYAMMLIGSLSLIGFPFRTGFYSKDVILELAY
TKYTISGNFAFWLGSVSVFFTSYYSFRLLFLTFLASTNSFKRDILRCHDAPILMAIPLI
FLAFGSIFVGYVAKV*

ND5 seems to have a frameshift in the beginning and the mapping of pacbio and 10x is kinda of perfect in the area

![](https://i.imgur.com/1l8inDT.png)



![](https://i.imgur.com/av04ScI.png)



## 9 dhQueRobu3
### 9.1 dhQueRobu3 MBG= 1001K

![](https://i.imgur.com/CilWF2s.png)


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### 9.2 dhQueRobu3 MBG= 5001K


![](https://i.imgur.com/dpjzCYl.png)

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### 9.1.1 Working to construct mito versions from MBG k=1001

1+,4+,5+,8+,6-,4-,2-,3+,9-,8-,7+,3-

Pacbio reads coverage:

![](https://i.imgur.com/j3N92qx.png)

![](https://i.imgur.com/QN6paKW.png)

![](https://i.imgur.com/PIbOK8Q.png)