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Showing top results for tag: mtDNA • reset
1
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342
views
How can you determine the mutation rate of mitochondrial DNA for your (Grasshopper) species?
pacBio numts mtDNA Genomics
updated 11 days ago by 20k • written 26 days ago by ▴ 40
0
votes
1
reply
344
views
Different insertion times from two methods
pacBio mtDNA NUMTS
updated 16 days ago by 44k • written 16 days ago by ▴ 40
0
votes
2
replies
657
views
What type of graph or visualization would be most appropriate to represent this data for effective comparison of insertion times across sequences?
pacBio NUMTs mtDNA Genomics
updated 16 days ago by 44k • written 20 days ago by ▴ 40
2
votes
2
replies
332
views
How can we determine or find the insertion time of Numts?
pacBio Bioinformatician mtDNA NUMTS
5 weeks ago by hashim.rana11 ▴ 40
0
votes
0
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197
views
How to plot phylogenetic tree(dendrogram) of mitochondria haplogroups?
phylogenetic haplogroups mtDNA dendrogram
8 weeks ago by Karibu • 0
0
votes
0
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182
views
Next Steps for NUMTs Identification and Analysis
pacBio Numts mtDNA
3 months ago by hashim.rana11 ▴ 40
1
vote
4
replies
479
views
How to construct Mitochondrial Haplotype network?
Mitochondrial Haplotype pacBio Network mtDNA
3 months ago by hashim.rana11 ▴ 40
1
vote
1
reply
310
views
How to calculate the Genetic Distance (P-Distance) by using mtDNA pacBio data?
pacBio Genetic-Distance mtDNA
3 months ago by hashim.rana11 ▴ 40
0
votes
0
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429
views
How to calculate the P-distance in Heteroplasmy Analysis Using mtDNA PacBio Data: Tools and Procedures
pacBio Heteroplasmy Somatic-mutations mtDNA
updated 3 months ago by 44k • written 3 months ago by ▴ 40
2
votes
3
replies
515
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity mtDNA PacBio
4 months ago by hashim.rana11 ▴ 40
0
votes
0
replies
211
views
Modify plot R mtDNA indel
plot mtDNA R
4 months ago by marco.barr ▴ 150
3
votes
4
replies
768
views
Why many organisms even though they possess mitochondrial DNA (mtDNA), it is not typically represented by chromosomes labeled as "mtDNA"?
genome mtDNA reference-genome sequence
6 months ago by George X. • 0
0
votes
11
replies
1.1k
views
mtDNA Cyclic Sequence Alignment CSAtool
mtDNA alignment CSA
updated 7 months ago by 145k • written 7 months ago by ▴ 150
1
vote
8
replies
1.6k
views
Mitochondrial genes - TPM calculation bulk RNA-Seq
TPM RNA-Seq mtDNA
10 months ago by nick_b55 ▴ 10
0
votes
0
replies
373
views
best annotator for mitochondria and heteroplasmy calculation
heteroplasmia mitochondria annotation mtDNA
10 months ago by toma.85 • 0
3
votes
2
replies
801
views
Mapping to mtDNA and then align the unmapped
mtDNA Alignment Samtools Bowtie2
14 months ago by DanielEB_fisk ▴ 20
0
votes
0
replies
497
views
Almost no peak output after peakcalling of mtDNA with MACS2
mtDNA python chip-seq MACS2
updated 19 months ago by 44k • written 19 months ago by • 0
0
votes
3
replies
1.3k
views
Removal of mitochondrial and chloroplast seqs from the assembly
chlpdna mtdna
updated 15 months ago by 44k • written 22 months ago by • 0
0
votes
1
reply
863
views
Remove Mitochondrial Reads from Genome reads
genomic genome mtDNA reads
updated 23 months ago by 145k • written 23 months ago by • 0
0
votes
0
replies
371
views
Core/pan genome pipeline
pangenome coregenome mtdna ngs Nanopore
2.4 years ago by schulpen_91 ▴ 30
2
votes
5
replies
3.1k
views
Some questions about call variants for mtDNA using GATK HaplotypeCaller
GATK HaplotypeCaller mtDNA
updated 2.4 years ago by ▴ 130 • written 6.1 years ago by ★ 1.4k
0
votes
0
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539
views
Human Mitochondrial Genome Feature Table for GenBank BankIt
GenBank Mitochondrial Genome submission mtDNA Feature Table Human BankIt
2.7 years ago by Tastulek • 0
0
votes
0
replies
473
views
mtDNA-seq by Capture-based hybirdization library method
mtDNA
2.9 years ago by Eric • 0
0
votes
0
replies
521
views
Different haplogrouping in graphical and text haplogrep results
graphviz lineage mtDNA haplogrep
3.3 years ago by irieljoerin ▴ 40
0
votes
0
replies
578
views
R package for AMOVA of mitochondrial haplotype frequencies
frequency haplotype AMOVA r mtDNA
3.4 years ago by irieljoerin ▴ 40
0
votes
0
replies
506
views
mtDNA variant calling
variant fasta seq mtdna
3.5 years ago by here_for_learning • 0
0
votes
0
replies
729
views
Method for estimation of subcontinental admixture from haplogroup data
haplogroup mtDNA Y chromosome admixture
3.8 years ago by irieljoerin ▴ 40
8
votes
16
replies
2.3k
views
How to check mitochondrial reference in GWAS data for HaploGrep analysis
gwas mtDNA snp haplogroup HaploGrep2
updated 3.9 years ago by 22k • written 4.0 years ago by ▴ 40
0
votes
2
replies
1.5k
views
Perform PCA for mtDNA MSA Data
mtDNA Haploid plink PCA mitochondrial genome
3.9 years ago by Tastulek • 0
0
votes
1
reply
563
views
Identifying Sequence data format
mtdna
4.4 years ago by RedaAlaoui • 0
5
votes
7
replies
1.4k
views
Strange coverage of mtDNA - need help interpreting MiSeq results
next-gen sequencing alignment igv mtdna
updated 4.6 years ago by 14k • written 4.6 years ago by ▴ 20
0
votes
0
replies
619
views
Association study mtDNA
mtdna association
4.7 years ago by felissia92 • 0
0
votes
1
reply
1.2k
views
mitochondrial DNA in vcf for haplogrep2
haplogrep2 mtDNA vcf
5.1 years ago by biosol ▴ 170
1
vote
4
replies
1.8k
views
Why snpEff annotation give different names to one same gene?
snpEff mtDNA
updated 5.9 years ago by ★ 17k • written 5.9 years ago by ★ 1.4k
0
votes
1
reply
1.8k
views
WGS for mtDNA variation
Assembly SNP sequencing mtdna
updated 5.9 years ago by 22k • written 8.0 years ago by ▴ 250
6
votes
7
replies
2.6k
views
Detection of mtDNA
next-gen-sequencing genome mtdna
updated 15 months ago by 44k • written 5.9 years ago by • 0
0
votes
4
replies
2.0k
views
Tools to detect CNV for NGS-mtDNA
mtDNA NGS
updated 15 months ago by 44k • written 6.1 years ago by ▴ 960
2
votes
1
reply
1.9k
views
How to apply GATK on mtDNA sequencing data?
GATK mtDNA
6.1 years ago by MatthewP ★ 1.4k
3
votes
4
replies
2.7k
views
How to download dataset from MITOMAP?
MITOMAP mtDNA database
6.2 years ago by MatthewP ★ 1.4k
3
votes
2
replies
1.3k
views
Do I need to mark duplicates for sequencing data using multiplex PCR to prepare library?
mtDNA picard multiplex PCR
updated 6.2 years ago by 16k • written 6.2 years ago by ★ 1.4k
5
votes
18
replies
3.8k
views
Some questions about write human mitochondrial variants into VCF file
VCF mtDNA
updated 6.3 years ago by 164k • written 6.3 years ago by ★ 1.4k
0
votes
0
replies
1.1k
views
How to analyse mtDNA insertion from NGS data?
mtDNA NGS indel
6.3 years ago by MatthewP ★ 1.4k
4
votes
7
replies
5.4k
views
Mitochondrial contamination over 90% in published atac-seq dataset.
atac-seq mtDNA bowtie2 mitochondrial contamination
6.8 years ago by daniele.avancini ▴ 70
1
vote
12
replies
3.0k
views
Detection of deletion for mitochondrial NGS analysis at position 3107
mitochondria NGS alignment mtDNA
updated 6.9 years ago by ★ 2.9k • written 6.9 years ago by ▴ 960
0
votes
0
replies
1.6k
views
Where can I find the HVR coordinates of mitochondrial DNA on the human genome?
mtdna hg19 hypervariable regions chrM haplogroup
7.5 years ago by Glen ▴ 30
4
votes
2
replies
2.0k
views
RNASeq differential expression: How to deal with few genes with extremely high expression levels
RNA-Seq mtDNA limma voom
updated 7.5 years ago by 8.8k • written 7.5 years ago by ★ 4.1k
2
votes
4
replies
2.4k
views
Heteroplasmy detection program
mtDNA
updated 2.8 years ago by 44k • written 10.2 years ago by ▴ 20
2
votes
11
replies
2.9k
views
Making a neighbor-joining tree of human populations based on mitochondrial DNA
human populations neighbor-joining tree mtDNA
updated 8.1 years ago by 8.7k • written 8.1 years ago by ▴ 60
0
votes
0
replies
1.1k
views
Looking for human mtDNA samples tagged tumor/normal
ncbi mtDNA
8.3 years ago by novice ★ 1.1k
1
vote
1
reply
3.0k
views
1000 genomes project mitochondrial DNA sequences
mtDNA sequence 1000genomes
updated 8.5 years ago by ▴ 370 • written 8.5 years ago by ▴ 70
50 results • Page 1 of 1
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Comment: Sankey + dot plot by zx8754 12k
What is the problem, where is the code you are trying? Provide code, example data, expected output.
Answer: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Michael 55k
Something went wrong during star alignments of samples OE1_2, OE1_3, and OE_NC_1. The obvious place to look for the reason is in the Star l…
Comment: How to compile Multiz by Pierre Lindenbaum 164k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to compile Multiz by Santex • 0
I'm sorry. I post a new question.
Comment: NeuronChat: identifyCommunicationPatterns_Neuron() error by sooni ▴ 20
I solved the problem by installing `NMF` package.
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
Can you check using `featureCounts` to make sure things look reasonable with alignments? You could also use `salmon` to do transcript quant…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
Since we don't have access to your data we can't comment. Check the integrity of your input data files. Validate the files if you are not s…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
https://www.biostars.org/u/145859/ : Use `ADD REPLY/ADD COMMENT` to add additional information to existing threads. `ADD YOUR ANSWER` is me…
Comment: How to compile Multiz by GenoMax 145k
Please do not ask questions unrelated to the original post in this thread. Post a new question.
Comment: How to compile Multiz by Santex • 0
I could install multiz from it! Thank you very much. Please help me out with the problem below. I run multiz like below. (myenv) tak…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
One of them looks okay, but I don't quite believe it. ```R > table(df$`intermediate_data.OE1_1_.genes.results`==0) FALSE TRUE 21200 2…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
It seems that the files that generated the results also have significant issues. Except for one sample, all other samples only have over 20…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
Their .fq files all look similar, should I rerun these programs?
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
> Cannot open intermediate_data/OE_NC_2_.temp/OE_NC_2__alignable_1.fq! It may not exist. Looks like you are missing some files. BTW this …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
The most torturous thing is that some groups did indeed generate results. ``` ls intermediate_data KO1_1_.stat KO1_3_.isoforms…
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