xBio.ca

Biology with the X factor.

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Data and reports

Runs

Processed data

Galaxy history: https://usegalaxy.org/u/verbal_cant/h/perumummyphase1
Current contents

BAMs of the bowtie2 alignments to hg38
SPAdes and MEGAHIT de novo assembly contigs
Normalized mtDNA VCF for Ancient0003

QC of samples, raw and processed

FastQC Raw forward reads, Ancient002 (SRR21031366)
FastQC Raw reverse reads, Ancient002 (SRR21031366)
FastQC Deduped/clumped/trimmed forward reads, Ancient002 (SRR21031366)
FastQC Deduped/clumped/trimmed reverse reads, Ancient002 (SRR21031366)
Bowtie2 flag stats for hg38 alignment, Ancient002 (SRR21031366)
Bowtie2 index stats for hg38 alignment, Ancient002 (SRR21031366)
QUAST Megahit assembly, Ancient002 (SRR21031366)
QUAST Spades assembly, Ancient002 (SRR21031366)
Busco Megahit assembly, Ancient002 (SRR21031366)
Busco Spades assembly, Ancient002 (SRR21031366)

FastQC Raw forward reads, Ancient003 (SRR20755928)
FastQC Raw reverse reads, Ancient003 (SRR20755928)
FastQC Deduped/clumped/trimmed forward reads, Ancient003 (SRR20755928)
FastQC Deduped/clumped/trimmed reverse reads, Ancient003 (SRR20755928)
Bowtie2 flag stats for hg38 alignment, Ancient003 (SRR20755928)
Bowtie2 index stats for hg38 alignment, Ancient003 (SRR20755928)
QUAST Megahit assembly, Ancient003 (SRR20755928)
QUAST Spades assembly, Ancient003 (SRR20755928)
Busco Megahit assembly, Ancient003 (SRR20755928)
Busco Spades assembly, Ancient003 (SRR20755928)
kraken2 classification Megahit assembly, Ancient003 (SRR20755928)
kraken2 classification SPAdes assembly, Ancient003 (SRR20755928)
QUAST Spades assembly, Ancient003 (SRR20755928)

FastQC Raw forward reads, Ancient004 (SRR20458000)
FastQC Raw reverse reads, Ancient004 (SRR20458000)
FastQC Deduped/clumped/trimmed forward reads, Ancient004 (SRR20458000)
FastQC Deduped/clumped/trimmed reverse reads, Ancient004 (SRR20458000)
Bowtie2 flag stats for hg38 alignment, Ancient004 (SRR20458000)
Bowtie2 index stats for hg38 alignment, Ancient004 (SRR20458000)
QUAST Megahit assembly, Ancient004 (SRR20458000)
QUAST Spades assembly, Ancient004 (SRR20458000)
Busco Megahit assembly, Ancient004 (SRR20458000)
Busco Spades assembly, Ancient004 (SRR20458000)

Binning results

checkm on metabat2 binning of Megahit assembly, Ancient002 (SRR21031366)
checkm on metabat2 binning of Spades assembly, Ancient002 (SRR21031366)
checkm on metabat2 binning of Megahit assembly, Ancient003 (SRR20755928)
checkm on metabat2 binning of Spades assembly, Ancient003 (SRR20755928)
checkm on metabat2 binning of Megahit assembly, Ancient004 (SRR20458000)
checkm on metabat2 binning of Spades assembly, Ancient004 (SRR20458000)

Motifs

MEME on spades assembly, Ancient003 (SRR20755928)
MEME on megahit assembly, Ancient003 (SRR20755928)
SEA on megahit assembly, Ancient003 (SRR20755928)

kraken2 (nt) taxonomy

Haplotype analysis, Ancient0003

- VCF qual stats on 100 million random samples Ancient003 (SRR20755928)
- 25th percentile: 44.9942
- 50th percentile: 68.9807
- 75th percentile: 110.995
- 90th percentile: 177.996
- Mean = 89.5416
- Std Dev = 61.7857
- Num Rows = 2.82063e+09

mtDNA ancient0003

HaploGrep output against MitoImpute database

Sample ID	Haplogroup	Rank	Quality	Range	Not Found Polys	Found Polys	Remaining Polys	AAC In Remainings	Input Sample
SRR20755928_sorted	M	1	0.8539	1-16569	4769G 10398G	73G 263G 489C 750G 1438G 2706G 7028T 8701G 8860G 9540C 10400T 10873C 11719A 12705T 14766T 14783C 15043A 15301A 15326G 16223T	152C (localPrivateMutation) 225A (localPrivateMutation) 3714G (localPrivateMutation) 12354C (localPrivateMutation) 15691G (localPrivateMutation) 16129A (localPrivateMutation) 16209C (localPrivateMutation) 16272G (localPrivateMutation) 16519C (hotspot)		73G 152C 225A 263G 489C 750G 1438G 2706G 3714G 7028T 8701G 8860G 9540C 10400T 10873C 11719A 12354C 12705T 14766T 14783C 15043A 15301A 15326G 15691G 16129A 16209C 16223T 16272G 16519C

Y-DNA haplotyping, ancient0003

ancient0003 Y-DNA yhaplo output