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Showing top results for tag: reference • reset
4
votes
6
replies
317
views
How to get 'chr' prefix hg38 reference genome
HG38 human reference chr
updated 9 days ago by 104k • written 9 days ago by • 0
2
votes
3
replies
153
views
Contigs and scaffold in reference genome
BWA Ensembl Genome Reference HiSat NCBI
updated 10 days ago by 104k • written 10 days ago by ▴ 370
3
votes
2
replies
149
views
adding a contig fasta to reference genome fasta
reference genome
updated 15 days ago by ★ 2.3k • written 18 days ago by • 0
2
votes
2
replies
160
views
Genotype imputation - do SNP IDs of input files and reference panels matter?
genotype SNP reference VCF imputation
updated 19 days ago by ▴ 830 • written 19 days ago by ▴ 160
2
votes
4
replies
238
views
Why are there nucleotides in the reference genome which are also minor alleles in the 1000 genomes project
reference genotype minor allele
updated 23 days ago by 45k • written 24 days ago by ▴ 60
2
votes
2
replies
141
views
How to know the positions of contigs in a reference genome
mapping positions alignment reference genome contigs
updated 4 weeks ago by 104k • written 4 weeks ago by ▴ 10
1
vote
2
replies
176
views
Fasta file for Whole exome sequencing analysis
Gencode WES file analysis Reference
4 weeks ago by tomer9w • 0
0
votes
1
reply
137
views
Downloading bacterial reference genome
reference genome
updated 5 weeks ago by 5.9k • written 5 weeks ago by • 0
4
votes
6
replies
285
views
RNA-seq for beginners
reference resequencing transcriptome gtf sequence gff
5 weeks ago by arko.bmb.du ▴ 20
0
votes
0
replies
110
views
Genome reference fpr variant annotation of deleterious variants?
variants reference genome annotation deleterious functional prediction
6 weeks ago by ja569116 • 0
0
votes
4
replies
563
views
GATK Input files reference and features have incompatible contigs: No overlapping contigs found.
reference gatk
5 weeks ago by Jordi • 0
2
votes
2
replies
172
views
Reference Genome dna, rm or sm??
unmaksed Reference masked genome
7 weeks ago by Akash D ▴ 10
0
votes
3
replies
185
views
Mapping fastq files to reference genome
fastq reference genome mapping
updated 7 weeks ago by ▴ 20 • written 7 weeks ago by ▴ 60
1
vote
1
reply
99
views
Sugarcane Rerence sequence Assembly
NGS reference Sugarcane transcriptome data genome
updated 8 weeks ago by 104k • written 8 weeks ago by • 0
0
votes
5
replies
297
views
Problem creating a reference genome
reference custom genome
9 weeks ago by lydiaiglesias • 0
1
vote
9
replies
456
views
RNAseq: Modify .fasta and .gtf files to add recombinant protein sequence
reference protein modify recombinant
10 weeks ago by Pavlos • 0
11
votes
7
replies
426
views
Why is human genome FASTA file on GENCODE much smaller than that on ENSEMBL?
reference genome GENCODE ENSEMBL
updated 9 weeks ago by 104k • written 11 weeks ago by ▴ 60
3
votes
9
replies
496
views
reference fasta creation
reference mapping fasta
11 weeks ago by geneart$$ ▴ 40
1
vote
1
reply
408
views
Merged Reference Panel using WES data
sequencing imputation reference
updated 11 weeks ago by ▴ 80 • written 20 months ago by • 0
4
votes
4
replies
391
views
Where to get consensus sequences of human transposable elements
database transposons reference
updated 3 months ago by 5.2k • written 3 months ago by 45k
0
votes
0
replies
140
views
how to build a graph reference with HISAT-genotype
reference RNA-seq hisat2 alignment
3 months ago by minghuiguo448 • 0
5
votes
2
replies
967
views
GRCm39 (mm39) vs GRCm38(mm10)
genome reference mouse DNA dna
updated 3 months ago by 104k • written 3 months ago by ▴ 10
0
votes
1
reply
196
views
What should be the value of Sjdboverhang in STAR?
STAR index reference sjdbOverhang
4 months ago by dare_devil ★ 1.4k
1
vote
5
replies
210
views
Human WGS :which genome reference
genome alignment reference
updated 5 months ago by 52k • written 5 months ago by • 0
0
votes
7
replies
234
views
subread keeps makes a weird .sam file, have i done something wrong?
subread rsubread alignment DNA reference
5 months ago by amy_houseman ▴ 20
10
votes
11
replies
15k
views
6 follow
How to determine reference genome that was used for alignment given BAM with obscure or no header
BAM Reference alignment Reference Genome
updated 5 months ago by ▴ 450 • written 6.1 years ago by ▴ 260
2
votes
4
replies
261
views
Sanger sequencing chromatogram aligned to reference gene
sanger sequencing chromatogram reference alignment
updated 6 months ago by ★ 1.6k • written 6 months ago by • 0
0
votes
3
replies
268
views
NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
MAF genome reference GRCm38 NCBI build
6 months ago by whb ▴ 20
1
vote
2
replies
205
views
How to create alternate reference for SNPs?
snps reference
8 months ago by Parham ★ 1.5k
2
votes
0
replies
448
views
Reference Consortium (HRC) in GRch38/hg38
haplotype reference genome
9 months ago by enho ▴ 20
1
vote
2
replies
418
views
Different reference human genome
bwa human reference
9 months ago by v.shapovalova1 ▴ 10
2
votes
4
replies
250
views
Changing the reference allele
population genomics reference ancestral allele
10 months ago by evoecogen • 0
7
votes
6
replies
3.3k
views
Problems For Mapping Contigs Onto Reference
blat reference genome
updated 11 months ago by 20 • written 10.3 years ago by ▴ 390
2
votes
1
reply
632
views
mouse chrY centromere location
genome reference
12 months ago by igor 12k
8
votes
14
replies
3.9k
views
List Of Dbsnp Variants Where Reference Genome Has Minor Allele
reference dbsnp variant exome
updated 15 months ago by 20 • written 9.6 years ago by ▴ 30
0
votes
7
replies
506
views
Reference sequence to be used for assembly in nanopore
reference Assembly
18 months ago by SUDOsundu ▴ 30
0
votes
1
reply
351
views
Problems with Reference alleles at VCF files
SNP vcf reference
20 months ago by epifaniarango • 0
2
votes
6
replies
755
views
Failure in extracting reads from bam file due to unknown reference
alignment bam extraction reference
20 months ago by marongiu.luigi ▴ 570
3
votes
4
replies
510
views
E coli Illumina paired assembly using a reference genome?
genome sequencing Assembly reference
23 months ago by lg248 • 0
0
votes
0
replies
372
views
reference peptide database (post-translational products)
peptides proteins reference database
23 months ago by gtrwst9 • 0
4
votes
3
replies
3.1k
views
Illumina Pe Reads Mapping To Reference Genome
illumina bowtie2 reference metagenomics
updated 2.1 years ago by 20 • written 8.4 years ago by • 0
0
votes
0
replies
763
views
Beagle phasing without map and reference parameters
beagle map reference
2.1 years ago by Shicheng Guo ★ 8.7k
0
votes
0
replies
513
views
How can I get the ID reference genes in GEO ?
ID reference GEO gene ID
2.3 years ago by Lila M ★ 1.1k
16
votes
7
replies
525
views
Why does UCSC produce reference genomes when GRC already does it well?
assembly reference
updated 2.3 years ago by 45k • written 2.3 years ago by ▴ 170
53
votes
14
replies
24k
views
9 follow
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
risk minor major reference alleles
updated 4 weeks ago by 75k • written 3.3 years ago by ▴ 320
0
votes
1
reply
398
views
high frequency protein truncating variants in hg19
reference genome annotation
updated 2.3 years ago by 45k • written 2.3 years ago by • 0
0
votes
0
replies
389
views
Are there any other reference alingnment bases than Balibase?
Balibase alignment reference databases
2.4 years ago by MichaelTrev ▴ 10
8
votes
9
replies
2.6k
views
7 follow
Assembling PacBio reads using a reference genome
PacBio Assembly Resequencing Reference
updated 2.5 years ago by ▴ 10 • written 4.0 years ago by ▴ 50
2
votes
2
replies
1.4k
views
Where can I find the reference files for the 1000 Genome project VCF data?
VCF 1000 Genome Reference
updated 2.5 years ago by 14k • written 2.5 years ago by ★ 1.5k
2
votes
5
replies
739
views
Finding and changing a given position in hg19 ref fasta file
hg19 fasta reference
2.6 years ago by cetin.m ▴ 50
50 results • Page 1 of 1
Recent Votes
Answer: What's the biggest thing you dislike about bioinformatics?
Comment: opening downloaded files from STRING protein network without R
Comment: What's the biggest thing you dislike about bioinformatics?
Gene Set Enrichment Analysis
Comment: Removing genes of Seurat object during integration pipeline
How to generate a .sam/.bam file of a particular chromosome or even a particular region?
How To Split A Bam File By Chromosome
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Answer: Would this laptop be sufficient for small dataset/sequence analysis? by Mensur Dlakic ★ 12k
16 GB of RAM will not cut it for any serious bioinformatics application these days. Doubly so if you choose to run Windows.
Comment: inquiry related to snpsift by Kevin Blighe 75k
I see - thanks. I am not sure that `SnpSift annotate` can do this, but you can first remove the original ID via `bcftools`, as follows: …
Answer: Forum: Job opportunities in Europe, with and without a PhD by Kevin Blighe 75k
South Africa? - very nice. I had been considering moving there, would you believe. There is no correct answer to your question, and one ca…
Comment: inquiry related to snpsift by rheab1230 • 0
the command: java -jar SnpSift.jar annotate dbSnp144.vcf variants.vcf > variants_annotated.vcf I am getting no error. the input file …
Comment: Displaying points which fall outside of the plot window in EnhancedVolcano by os306 ▴ 10
Hi there, just to follow up on this, I used your package to generate my volcano plots and got exactly what I was looking for. I now wish to…
Comment: inquiry related to snpsift by Kevin Blighe 75k
Hi, please show: 1. the command(s) that you are using 2. a sample of your input data 3. a sample of your output data 4. any status, wa…
Comment: opening downloaded files from STRING protein network without R by fionajcunningham • 0
thanks GenoMax I will try this sorry for delay in reply!! Fiona
Comment: What's the biggest thing you dislike about bioinformatics? by WouterDeCoster 45k
The alternative, constant off-by-one errors, aren't my idea of fun either :-)
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
Yeah, you can filter min_cells in Seurat with SCtransform. That would probably change the gene numbers in the SCT assay of the object. I u…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
Doesn't sctransform has a `min_cells` parameter that you could use here? It will only consider genes detected in at least `min_cells` cells…
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
I was thinking of making it an arbitrary cut off of 10 cells, Seurat's documentation uses 3 for reading in a single sample. I believe that …
Answer: How To Split A Bam File By Chromosome by etiennedanis • 0
With samtools v1.11, ```samtools view -b in.bam chr1 > out.bam``` did not work for me. But ```samtools view -b in.bam 1 > out.bam``` wo…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
What is a "few" cells? So how many? You would need to manually calculate the fraction of cells expressing a certain gene. Not sure in which…
Comment: I want to make a graph for conserved regions by sa.youssef • 0
Thanks so much, it is a great suggestion. may I ask you if you know a way to visualize the results of these data in my report? as we are wo…
Comment: Minfi - estimateCellCounts by Papyrus ★ 1.1k
I understand that you have whole blood samples and that's why you expect them to have more granulocytes? You could also try the [ENmix][1] …
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