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Filtering for tag: consensus • reset
0
votes
0
replies
277
views
Deletions are missed from consensus sequence even when they are predominant. Is this common to vcf2fq of vcfutils?
vcf2fq consensus bcftools indel
23 days ago by malaya77 • 0
29
votes
11
replies
3.7k
views
7 follow
Tutorial: Generating consensus sequence from bam file
bam fasta consensus Tutorial
updated 6 weeks ago by • 0 • written 2.1 years ago by 14k
0
votes
0
replies
202
views
PacBio's variantCaller's vcf inconsistent with it's consensus sequence
pacbio variant variantCaller vcf consensus
updated 4 months ago by 20 • written 5 months ago by ▴ 40
0
votes
2
replies
182
views
FASTA file header
consensus
5 months ago by storm1907 • 0
0
votes
1
reply
264
views
How to generate a Consensus sequence from SRA BLAST output from web server?
consensus sequence sra blast NGS
6 months ago by lokdeep17 • 0
0
votes
2
replies
193
views
Ambiguous places in consensus
biopthon consensus ambiguous dumb_consensus
8 months ago by adrian18_07 ▴ 10
0
votes
2
replies
297
views
How to make consensus sequences for a list?
consensus biopython
9 months ago by adrian18_07 ▴ 10
0
votes
1
reply
193
views
conservative position extraction
sequence consensus conservative fastq parsing
updated 11 months ago by 12k • written 11 months ago by • 0
0
votes
9
replies
1.2k
views
get consensus sequence from bam file with insertions
consensus
updated 12 months ago by ▴ 10 • written 23 months ago by • 0
5
votes
6
replies
769
views
Methods for Doing Consensus Variant Calling between multiple callers
WES DNA Consensus Variant Calling
18 months ago by djevanclark ▴ 40
3
votes
3
replies
275
views
How are high phred scores represented?
consensus assembly
updated 21 months ago by ★ 2.7k • written 21 months ago by ▴ 170
0
votes
0
replies
594
views
Consensus genotype of MUTECT1, MUTECT2, Varscan, Muse and Somaticsniper
consensus mutation bcftools
21 months ago by Shicheng Guo ★ 8.6k
3
votes
4
replies
1.6k
views
bcftools mpileup --max depth : What would be a reasonable setting for this option?
bcftools mpileup consensus
23 months ago by Cookie-san ▴ 110
1
vote
1
reply
1.1k
views
Calling haploid consensus sequence from vcf
vcf samtools bcftools consensus haploid
updated 23 months ago by 72k • written 24 months ago by • 0
1
vote
3
replies
2.5k
views
customized clusterAlg of NMF in consensusClusterPlus
R NMF consensus cluster
updated 24 months ago by 20 • written 3.4 years ago by ▴ 60
0
votes
7
replies
937
views
Does SPAdes produce consensus sequence?
consensus Assembly
2.0 years ago by DanielC ▴ 140
0
votes
0
replies
419
views
Gaps in sequenced DNA consensus generated from contigs
gaps consensus contigs
2.0 years ago by DanielC ▴ 140
0
votes
2
replies
546
views
Identifying consensus sequence between multiple Arabidopsis genome sequences
Alignment Consensus SNPs Variations Plant
2.3 years ago by bioinforesearchquestions ▴ 280
2
votes
4
replies
1.8k
views
The fasta sequence does not match the REF allele at chr1:1298836 ?
bcftools vcf consensus
2.3 years ago by RobertUt ▴ 30
3
votes
4
replies
1.7k
views
How to get consensus FASTA sequence from GFA assembly graph?
gfa consensus
2.3 years ago by shenwei356 5.8k
2
votes
10
replies
1.8k
views
bcftools mpileup no output (empty calls.bcf file)
bcftools samtools mpileup consensus calls.bcf
2.3 years ago by RobertUt ▴ 30
0
votes
3
replies
1.1k
views
How to get a consensus of the contigs obtained from an assembler like spades?
contigs consensus spades
2.3 years ago by DanielC ▴ 140
3
votes
4
replies
2.0k
views
Majority consensus from bam file
consensus alignment
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by ▴ 10
0
votes
6
replies
554
views
Should I replace heterozygous variants to make a consensus
Variant Consensus Genome assembly Heterozygous
2.5 years ago by deepti1rao ▴ 30
2
votes
5
replies
1.3k
views
Merge multiple overlapping consensus sequences
assembly consensus
updated 2.6 years ago by 32k • written 2.8 years ago by ▴ 70
0
votes
2
replies
1.6k
views
Generate Consensus Sequence from Pairwise Alignment
alignment Consensus Blast
2.8 years ago by kspata ▴ 70
3
votes
4
replies
2.7k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus sequencing noise OpenGene Tutorial
2.9 years ago by chen ★ 2.1k
4
votes
4
replies
2.8k
views
Does vcf-consensus support indels?
consensus vcf-consensus
updated 3.0 years ago by ▴ 60 • written 5.1 years ago by ▴ 290
4
votes
9
replies
8.6k
views
7 follow
How To Get Consensus Sequence Including Variant From A Vcf File For Several Individuals...?
vcf consensus gatk variant calling
updated 3 days ago by • 0 • written 8.5 years ago by ★ 1.0k
1
vote
5
replies
1.7k
views
Consensus Sequence And Assembly Of Multiple Group Of Sequences
consensus
updated 3.2 years ago by 20 • written 7.5 years ago by 9.3k
3
votes
7
replies
2.0k
views
Tune criteria for extraction of consensus sequence from bam/sam alignment
bam sam consensus bcftools vcfutils
3.2 years ago by al-ash ▴ 150
1
vote
1
reply
1.5k
views
consensus sequence of complex estructural variants
consensus estructural variant
updated 3.3 years ago by 20 • written 6.2 years ago by ▴ 290
2
votes
2
replies
5.2k
views
fgbio: Calling consensus reads using UMI
fgbio consensus
updated 3.3 years ago by ▴ 60 • written 3.3 years ago by 9.3k
0
votes
1
reply
924
views
Consensus sequences with reference allele instead of missing
bcftools consensus missing bases
3.4 years ago by agathejouet • 0
2
votes
2
replies
1.0k
views
all posible sequences from consensus
sequence python consensus TSS DNA
updated 3.4 years ago by 135k • written 3.4 years ago by • 0
1
vote
4
replies
751
views
Making seq chimeras and concatenation in protein MSAs
alignment concatenation consensus consambig emboss
3.4 years ago by roussine ▴ 10
8
votes
11
replies
4.6k
views
How To Merge Consensus Motif To Degenerate Motif ? [Motif Merge Or Motif Clustering]
motif merge clustering consensus
updated 3.5 years ago by 20 • written 8.1 years ago by ▴ 110
0
votes
5
replies
2.0k
views
Pipeline design: from reads to consensus sequences of multiple individuals
pipeline mapping alignment variant consensus
3.6 years ago by agathejouet • 0
7
votes
3
replies
1.2k
views
Conflicting consensus sequences from different tools (bug in hmmemit?)
hmm consensus bipython python
updated 3.6 years ago by ▴ 150 • written 3.6 years ago by 19k
1
vote
2
replies
979
views
Which strategy to get draft genome: rawread mapping or de novo assembly?
consensus Assembly genome
3.6 years ago by curiousbiologist ▴ 40
3
votes
2
replies
1.5k
views
Consensus fasta file with uncovered bases set to Ns
reference genome BED fasta consensus
updated 3.6 years ago by 9.5k • written 3.6 years ago by ▴ 30
1
vote
11
replies
2.0k
views
Extract consensus dna sequence of multiple genes from multiple bam files in fasta format
samtools fasta genes bam consensus
3.6 years ago by bioinfo8 ▴ 150
11
votes
1
reply
2.5k
views
Merge Scaffolds From Different Individuals?
assembly contigs consensus
3.7 years ago by Gabriel R. ★ 2.8k
3
votes
3
replies
1.4k
views
Protein Sequence Analyses
protein sequence consensus
updated 3.8 years ago by ★ 1.9k • written 3.8 years ago by ▴ 70
0
votes
1
reply
1.5k
views
how do I get a wonderful genome draft? : gap closed step
draft genome gap closed consensus
3.8 years ago by vmicrobio ▴ 270
4
votes
4
replies
948
views
Clumpify : issues with consensus mode (reverse complement of R1)
clumpify consensus
updated 3.8 years ago by 17k • written 3.8 years ago by 9.3k
5
votes
1
reply
2.9k
views
generating a reasonable consensus with bcftools + vcf-consensus
SNP consensus bam
4.0 years ago by mths_b ▴ 40
2
votes
3
replies
1.7k
views
IUAPC codes in consensus sequence ? samtools mpileup / bcftools call / bcftools consensus
bcftools consensus IUAPC
updated 4.1 years ago by 135k • written 4.1 years ago by ▴ 30
0
votes
0
replies
985
views
Trying to align Stride sequences and find consensus sequence
Stride alignment consensus
4.2 years ago by ericbrenner • 0
1
vote
2
replies
2.2k
views
Generating consensus sequences
consensus fasta bwa vcftools
updated 4.4 years ago by ▴ 270 • written 4.4 years ago by ▴ 200
109 results • Page 1 of 3
Recent Votes
Answer: Creating reference genome for mapping and then selecting
Comment: Creating reference genome for mapping and then selecting
Answer: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Answer: Tool to find chromosome specific repeats
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Recent Replies
Answer: Expression of gene of interest across conditions in single-cell data by jared.andrews07 9.1k
Take a look at [dittoSeq](http://www.bioconductor.org/packages/release/bioc/vignettes/dittoSeq/inst/doc/dittoSeq.html) for viz options - it…
Comment: Extracting only tumor samples from Single cell RNASeq by jared.andrews07 9.1k
You need pre-defined variants for Vartrix. Typically it's used in conjuction with WGS/WES from bulk tissue to look for clonal variants in d…
Comment: Cell composition in each condition of single cell data by paria.alipour ▴ 20
Oh, I'm sorry. I already posted it in here the https://www.biostars.org/p/457243/#9464486. I've added the images
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens by Quanyou • 0
This seems OK when one gene generates only one transcirpt. But when one gene has multiple transcripts, these code would return a table wher…
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens by Quanyou • 0
This seems feasible. But I want to convert tens of thousands of transcript IDs. Could you tell me how can I make it through sequene search?
Answer: bbmap, mapq and uniquelly mapped reads filtering by GenoMax 99k
Many threads exist that show how to extract uniquely mapped reads. Here are a couple of examples:<br> https://www.biostars.org/p/276216/#27…
Comment: Cell composition in each condition of single cell data by rpolicastro 5.1k
The images seem to be missing from your post
Comment: Limma experiment design and making contrasts by kra277 • 0
Thank you very much for this. Much appreciated.
Comment: Limma experiment design and making contrasts by Kevin Blighe 72k
Hi, these follow the same principles as formulae used in regression modelling, so, you may want to focus on that (when searching). What lim…
Comment: Limma experiment design and making contrasts by kra277 • 0
That is very insightful. Thank you very much for the answer. Also, if I may ask, could you please point me to the articles for understandin…
Comment: Keep values from VCF file into Ensembl VEP annotation by brunobsouzaa ▴ 510
Thanks Man... I've wroten a simple awk command for this task! Everything is working fine.
Comment: Raw read processing using trimmomatic by boczniak767 ▴ 740
Do you have exact command used by the author? I guess that not all details was presented in the paper. You can always ask the corresponding…
Comment: should stop codon be counted as part of CDS by sullis02 • 0
Your github page appears to live here now https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gxf.md
Comment: How do I compare degree and betweenness centrality for different PPI networks? by Istvan Albert 87k
I am not all that knowledgeable of Cytoscapes features and scripting capabilities, but if it does not support that operation you can expo…
Comment: Creating reference genome for mapping and then selecting by Istvan Albert 87k
you would get the counts as you would get them in any other case, how do you know something maps to chromosome 1 of human genome? Because i…
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