---
# System prepended metadata

title: ddAraThal4

---

# ddAraThal4

- Auto-generated Table of Content
[ToC]


# 1 ddAraThal4

## 1.1. MBG k=1001

```/lustre/scratch124/tol/projects/darwin/data/dicots/Arabidopsis_thaliana/working/mito_chloro_mbg```

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


## 1.2 Chloroplast by hand
```
biopython) mu2@tol-head2:/lustre/scratch124/tol/projects/darwin/data/dicots/Arabidopsis_thaliana/working/mito_chloro_mbg$ python /software/team311/mu2/join_segments.py NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa chloro.paths NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa chloro.paths.joined.fasta
```

3+, 2-, 1-, 2+



## 1.3 Chloroplast annotation 


So what I did for now (on 19.1.) was:

SSC-IRb-LSC-IRa


Ok - First let me rotate such it starts at psbA

126760..127821
gene="psbA"

```mu2@tol-head1:/lustre/scratch124/tol/projects/darwin/data/dicots/Arabidopsis_thaliana/working/mito_chloro_mbg/mitohifi-chloro/PGA/target-nonrotated$ python /software/team311/mu2/MitoHiFi/scripts/rotate.py -i cloro.annotation_mtDNA_contig.fasta -r 126760 > cloro.annotation_mtDNA_contig.rot.psbA.fasta
INFO: rotating each sequence record 126760 bp clockwise...

INFO: cloro sequence (154474 bp) was rotated 126760 bp.
```



Lucia says chloroplast orientation should be:

LSC-IR1-SSC-IR2 + making sure that the orientation of SSC is such that it ends with  ycf1 and LSC starts at psbA


what she wants is:
1-,2+, 3-, 2-

```
(biopython) mu2@tol-head1:/lustre/scratch124/tol/projects/darwin/data/dicots/Arabidopsis_thaliana/working/mito_chloro_mbg$  python /software/team311/mu2/join_segments.py NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa chloro-order NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa chloro-order.fa
Collecting sequences from NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa
Reading links from NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa
=======================================
Processing  1-,2+,3-,2-
1- 2+
================== Basic step
1- 2+ 1435M
From cigar 1435
Added coordinates: [87033 - 111870)
2+ 3-
================== Basic step
2+ 3- 1455M
From cigar 1455
Added coordinates: [111870 - 131092)
3- 2-
================== Basic step
3- 2- 1455M
From cigar 1455
Added coordinates: [131092 - 155909)
Writing chloro
```

# 1.4 Lucia's requested order

1+,2+,3-,2-
```
mu2@tol-head2:/lustre/scratch124/tol/projects/darwin/data/dicots/Arabidopsis_thaliana/working/mito_chloro_mbg$ python /software/team311/mu2/join_segments.py NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa chloro-order2 NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa chloro-order2.fa
Collecting sequences from NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa
Reading links from NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa
=======================================
Processing  1+,2+,3-,2-
1+ 2+
================== Basic step
1+ 2+ 1435M
From cigar 1435
Added coordinates: [87033 - 111870)
2+ 3-
================== Basic step
2+ 3- 1455M
From cigar 1455
Added coordinates: [111870 - 131092)
3- 2-
================== Basic step
3- 2- 1455M
From cigar 1455
Added coordinates: [131092 - 155909)
Writing chloro
```

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



# 2. Mitochondria

Going manually across the graph following the path bellow:

4-,6+, 9-, 7-, 5-, 6+, 8-, 7-

The used joing_segments (Sergey's code) to merge and create a fasta

```
(biopython) mu2@tol-head1:/lustre/scratch124/tol/projects/darwin/data/dicots/Arabidopsis_thaliana/working/mito_chloro_mbg$ python /software/team311/mu2/join_segments.py NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.fa mito_mu2 NC_037304.1.MZ323108.1.fasta.BOTH.HiFiMapped.bam.filtered.1k.gfa mito_mu2.fa
```
Then ran mitohifi to final circularization of the extremities and automated annotation.

Mitohifi run:

```
/lustre/scratch124/tol/projects/darwin/data/dicots/Arabidopsis_thaliana/working/mito_chloro_mbg/mitohifi_mito_mu2
```


General result is good:

```
# Related mitogenome is 367808 bp long and has 58 genes
contig_id       frameshifts_found       genbank_file    length(bp)      number_of_genes
final_mitogenome        rpl2    final_mitogenome.gb     368831  60
```

## 2.1 Mapping view of mitochondria

Mapping view is very clean

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

Where are these files?

```
/lustre/scratch124/tol/projects/darwin/data/dicots/Arabidopsis_thaliana/working/mito_chloro_mbg/mitohifi_mito_mu2/mapping/mito_mu2_rotated.bam 
```

samtools flagstat

19581 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
19581 + 0 mapped (100.00% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

The above results was a mapping having both, the assembled mitochondria and chloroplast sequences as references.

