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Important Files_11436064
Created by Robert Ness, last modified on Jul 17, 2018
For reference-based analyses in Chlamydomonas reinhardtii we use the version 5.3 genome from Phytozome. It was created by JGI. The reference did not originally include the plastid or mitochondrial genomes. It would be problematic to align sequence reads to the genome without these organelle genomes because the organelle-derived reads may erroneously align to the nuclear genome. Similarly, the reference genome is based on strain CC-503 which happens to be a mating type plus strain. That means when we map MT- strains to the reference their MT- specific genes will not be mapped. To avoid this I have added the organelle genomes and the MT- allele.
This is the actual sequence in fasta format. The chromosomes 1 to 17 are labelled "chromosome_1, chromosome_2...chromosome_17". The organelles are named cpDNA and mtDNA for chloroplast and mitchondrial genomes respectively. The mtMinus locus excluding the rest of chromosome 6 is called mtMinus.
/scratch/research/references/chlamydomonas/5.3_chlamy_w_organelles_mt_minus/chlamy.5.3.w_organelles_mtMinus.fasta
If you want to know where the genes are the annotation of all genes including those in the organelles and MT- are found here:
/scratch/research/references/chlamydomonas/5.3_chlamy_w_organelles_mt_minus/annotation/concatenated_GFF/final.strict.GFF3
Annotation table
I have also created a large table which documents many genomic features of the Chlamydomonas reference genome where each site in the reference genome is represented by a line of the file. It's pretty much a big table. The columns of the table are documented in the header of the file with lines that start with ##
/scratch/research/references/chlamydomonas/5.3_chlamy_w_organelles_mt_minus/annotation/concatenated_GFF/annotation_table.txt.gz
Quebec is the only area where there are many samples from a single geographic area. There are two samples, 4 that start with CC-293[5678] and 20 that start with CC-30[5678][0-9]
All the quebec samples from the set of natural strains that start with CC-30
/scratch/research/data/chlamydomonas/quebec/Individual.InDelRealigned.BAMs
The combined bam of CC-30’s is here
/scratch/research/data/chlamydomonas/quebec/BAMs/quebec_wt.realigned.bam
I refer to all natural strains excluding CC-30’s as the species-wide sample. This is in reference to the fact that these samples range from Florida, to Minnesota to Quebec.
Notes- there is reason to believe that CC-2932 has been contaminated with another algal species (personal communication with Rory Craig) - we can instead use the Jang et al version of that strain (see below)
Individual BAMs
/scratch/research/data/chlamydomonas/species_wide/Individual.InDelRealigned.BAMs
Combined BAM
/scratch/research/data/chlamydomonas/species_wide/BAMs/species_wide.realigned.bam
Jang and Ehrenreich Sequence
**in Jang H, Ehrenreich IM (2012) Genome-Wide Characterization of
Genetic Variation in the Unicellular, Green Alga Chlamydomonas
reinhardtii. PLoS ONE 7(7): e41307.
https://doi.org/10.1371/journal.pone.0041307 the
authors sequences a bunch of the same wildtype C. reinhardtii. I've
downloaded those onto HPCNODE1 here and they can be used especially
because they have longer reads.
**
/scratch/research/data/chlamydomonas/species_wide/Individual.InDelRealigned.BAMs
Within this folder there are combined BAMs for each of the 6 ancestral strains There is also one folder for each of the 6 ancestral lines where each of the MA lines has an independent BAM
/scratch/research/data/chlamydomonas/bgi_full_MA/realigned_bams
all_quebec VCF has ALL 24 Quebec strains - 4 x CC293[5678] and 20 x
CC30[5678][0-9]
/scratch/research/data/chlamydomonas/quebec/VCFs/all_quebec.HC.vcf.gz
The quebec one is only the 20 x CC-30[5678][0-9]
/scratch/research/data/chlamydomonas/quebec/VCFs/quebec.HC.vcf.gz
The species wide VCF includes all wild strains excluding the CC30's This VCF was called using HaplotypeCaller in haploid mode:
/scratch/research/data/chlamydomonas/species_wide/VCFs/species_wide.HC.vcf.gz
This one is called using the older UnifiedGenotyper in diploid mode.
/scratch/research/data/chlamydomonas/species_wide/VCFs/species_wide.UG_2N.vcf.gz
The 20 quebec CC-30[5678][0-9] strains are here:
/scratch/research/data/chlamydomonas/quebec/fastq/CC3068_wt.2.fq.gz
- additional Quebec strains CC-29"s are found in species wide...
Species-Wide
Each of the species-wide strains are found in their own folder here:
/scratch/research/data/chlamydomonas/species_wide/fastq/
These samples were given to us by collaborators from NYU - they have slightly different names - starting with CR but the numbers (eg CR-2344) are equivalent.
Document generated by Confluence on May 22, 2024 11:44
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