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122,201 results • Page 666 of 2445
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4
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4
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2.3k
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Obtaining variant allele frequencies with the Ensembl API
perl Ensembl API variant frequency
updated 4.6 years ago by 24k • written 4.6 years ago by ▴ 110
0
votes
0
replies
859
views
How to analyze MBD-Seq data?
CpG methyl islands MBD-Seq methylation
4.6 years ago by dagsbio ▴ 20
0
votes
2
replies
1.5k
views
ngs MiSeq pipeline vs GATK best practices
pipeline gatk MiSeq ngs
updated 4.6 years ago by ▴ 10 • written 4.6 years ago by • 0
1
vote
2
replies
1.5k
views
problem in installing primer3 in ubuntu
primer3
updated 3.3 years ago by 45k • written 4.6 years ago by • 0
1
vote
2
replies
1.3k
views
Comparing millions of trimmed reads to large database
bowtie2 blastn
updated 4.6 years ago by 35k • written 4.6 years ago by ▴ 140
0
votes
1
reply
1.1k
views
Trio haplotype information in the 1000 Genome Project
pedigree phasing haplotypes trio human
updated 4.6 years ago by 2.9k • written 4.6 years ago by • 0
1
vote
1
reply
987
views
how to create an interval file to extract sequences?
bedtools sequences blast fasta
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
0
votes
1
reply
2.1k
views
How to find the standard error when the GWAS summary data does not provide?
GWAS SE
updated 4.6 years ago by ▴ 940 • written 4.6 years ago by • 0
2
votes
4
replies
1.3k
views
Can anyone suggest resources for troubleshooting why my alignment using Bowtie1.1.1 is incorrect?
flagstat Bowtie1.1.1 samtools
4.6 years ago by nessj • 0
2
votes
3
replies
1.5k
views
SNPs coordinates for each read
SNPs mutation Coordinate BAM read
4.6 years ago by mante93 • 0
0
votes
6
replies
3.1k
views
What is the output of rna-seq alignment to reference transcriptome (FASTA+GTF) look like in SAM format?
RNA-seq aligment nanopore
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
0
votes
2
replies
1.7k
views
Working with multiple bam files from tumour vs normal samps in VarScan Somatic
Variants DNA-seq Galaxy VCF
4.6 years ago by rodolfo.peacewalker ▴ 390
0
votes
2
replies
2.0k
views
Sequence divergence of whole genomes
alignment divergence
4.6 years ago by Colaptes ▴ 120
2
votes
5
replies
3.1k
views
switch off warning in blast command line
efetch ensembl warnings
updated 4.6 years ago by ★ 30k • written 4.6 years ago by ▴ 770
2
votes
4
replies
2.3k
views
Increase the input sequences in pfamScan
PfamScan
4.6 years ago by K.Gee ▴ 40
12
votes
8
replies
5.6k
views
DESeq2 design for two variables and pairwise comparisons
deseq2 contrasts rnaseq LRT
updated 3.7 years ago by ★ 1.3k • written 4.6 years ago by ▴ 230
2
votes
6
replies
2.2k
views
Comparing genomes against randomized genomes
sequence genomes
4.6 years ago by schlogl ▴ 180
0
votes
0
replies
603
views
Separate BAM reads by the number and type of mismatchs on the read
samtools pysamtools bam rna-seq
4.4 years ago by Anna-Leigh • 0
0
votes
2
replies
957
views
Genome Dataset (include nucleotide string)
cancer-genome
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
0
votes
0
replies
1.0k
views
Alternative free software for recombination rate estimation ?
radseq joinmap stacks
4.6 years ago by Picasa ▴ 700
0
votes
0
replies
917
views
Reproduce single-variant score test
logistic score Rvtest single-variant SNP
4.6 years ago by vincentpluimakers • 0
1
vote
0
replies
806
views
Extracting length of deletions from a specific region from a BAM file
Nanopore indels
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 60
1
vote
2
replies
3.5k
views
pheatmap troubles...!!
gsva R Rstudio pheatmap heatmap
updated 4.6 years ago by ▴ 220 • written 4.6 years ago by • 0
2
votes
4
replies
1.7k
views
What is the resolution of microbial sequence assembly
microbiome SPAdes assembly species
updated 4.6 years ago by ▴ 130 • written 4.6 years ago by ▴ 770
5
votes
2
replies
2.1k
views
High confident germline SNP and INDELS for VQSR for reference genome GRCh37
INDEL SNP 1000g GRCh37
4.6 years ago by nhaus ▴ 420
0
votes
0
replies
981
views
Is my use of mapfromtranscripts correct in GenomicFeatures package? converting cDNA coordinates to genomic coordinates with GenomicFeatures
bioconductor genomicfeatures r rna22
4.6 years ago by anon • 0
0
votes
3
replies
2.1k
views
How to convert GFF3 file into tbl file
python
updated 4.6 years ago by 16k • written 4.6 years ago by ▴ 80
2
votes
1
reply
1.2k
views
IGH on Ensembl
Ensembl IGH
updated 4.6 years ago by 24k • written 4.6 years ago by ▴ 20
1
vote
2
replies
1.9k
views
SynChro input files
SynChro
updated 2.7 years ago by 45k • written 6.8 years ago by ▴ 30
4
votes
3
replies
1.8k
views
What Phenotype databases do you recommend for searching genes related to diseases?
disease phenotype databases
updated 4.6 years ago by ▴ 20 • written 4.8 years ago by ▴ 10
2
votes
1
reply
1.3k
views
How to submit 60 bed files for one rule in Snakemake as an input file
gatk snakemake
4.6 years ago by kamanovae ▴ 100
0
votes
1
reply
802
views
RefSeq obtained from genome.ucsc.edu
Genome-browser Annotation sequence
updated 2.7 years ago by 45k • written 4.6 years ago by ▴ 320
1
vote
1
reply
863
views
What type of data should I search for to do a GWAS
Data Gene SNP GWAS
updated 4.6 years ago by 12k • written 4.6 years ago by • 0
0
votes
1
reply
1.1k
views
Export ensembl efetch in comma-delimited format
format efetch ensembl
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 770
0
votes
5
replies
2.0k
views
Merging two linux files based on same rows
rsID coordinates plinkfile Merge
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 70
0
votes
0
replies
812
views
Job: Senior Staff Bioinformatician at the University of Melbourne Centre for Cancer Research
cancer genomics
4.6 years ago by Oliver • 0
47
votes
12
replies
43k
views
9 follow
What is a gene transcript?
sequencing ensembl gene transcript
updated 4.6 years ago by • 0 • written 8.7 years ago by ▴ 110
0
votes
1
reply
964
views
Chosing a phylogenetic tree construction method
tree phylogenetic method
updated 4.6 years ago by ▴ 120 • written 4.6 years ago by ▴ 180
0
votes
1
reply
1.7k
views
error in snakemake
gatk snakemake
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 100
0
votes
0
replies
607
views
Role of the 'Known resource' in VQSR
GATK gatk VariantRecalibrator VQSR
4.6 years ago by SBM_Han • 0
2
votes
4
replies
2.9k
views
Looping in R to perform a GSEA analysis
RNA-Seq GSEA loops R
updated 4.6 years ago by 90k • written 5.1 years ago by ▴ 390
1
vote
2
replies
1.1k
views
bedtools error
bedtools bash
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
0
votes
4
replies
1.6k
views
How to read a series matrix into R
R GEO seriesmatrix Expressionmatrix
4.6 years ago by waveafterwave • 0
0
votes
0
replies
760
views
PAML/CODEML: which sites are selected in site model?
paml codeml
4.6 years ago by DNAlias ▴ 40
2
votes
2
replies
1.9k
views
DNA vs RNA seq for microbiome
microbiome rnaseq sequencing
updated 4.6 years ago by ★ 2.2k • written 4.6 years ago by ▴ 120
0
votes
0
replies
800
views
What size regions to use for motif Identification from differential H3K27ac peaks ?
H3K27ac homer motif
4.6 years ago by gkunz ▴ 30
2
votes
2
replies
1.9k
views
how to find different expressed genes in GEO2R and do I have to apply a process to the results I get from GEO2R
genes venn expressed different GEO2R
4.6 years ago by eckmk ▴ 10
6
votes
12
replies
18k
views
11 follow
Forum: Online/remote/distance learning/ - partime/fulltime - PhD, Bioinformatics in USA
PhD university
updated 2.7 years ago by 45k • written 9.2 years ago by ▴ 20
1
vote
5
replies
2.5k
views
hisat2 error
hpc hisat2
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 40
0
votes
4
replies
2.5k
views
biomart returns several ensembl ids for one gene
scrna-seq ensembl biomart r
4.6 years ago by fifty_fifty ▴ 90
122,201 results • Page 666 of 2445
Recent Votes
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
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Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets by GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
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