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122,201 results • Page
666 of 2445
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Votes
Replies
4
votes
4
replies
2.3k
views
Obtaining variant allele frequencies with the Ensembl API
perl
Ensembl
API
variant
frequency
updated 4.6 years ago by
Emily
24k • written 4.6 years ago by
robles.daniela
▴ 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
tadeja.klade
▴ 10 • written 4.6 years ago by
tinakopale
• 0
1
vote
2
replies
1.5k
views
problem in installing primer3 in ubuntu
primer3
updated 3.3 years ago by
Ram
45k • written 4.6 years ago by
Dr. Kaushal Pratap
• 0
1
vote
2
replies
1.3k
views
Comparing millions of trimmed reads to large database
bowtie2
blastn
updated 4.6 years ago by
h.mon
35k • written 4.6 years ago by
geneticatt
▴ 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
4galaxy77
2.9k • written 4.6 years ago by
Jesper
• 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
GenoMax
154k • written 4.6 years ago by
crissavega23
• 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
Lemire
▴ 940 • written 4.6 years ago by
mscpythonstudy
• 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
GenoMax
154k • written 4.6 years ago by
sonsunjirachote
• 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
Mensur Dlakic
★ 30k • written 4.6 years ago by
marongiu.luigi
▴ 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
1769mkc
★ 1.3k • written 4.6 years ago by
bioinfo8
▴ 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
Ram
45k • written 4.6 years ago by
ysnerdgn_38
• 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
GenoMax
154k • written 4.6 years ago by
a.beggs
▴ 60
1
vote
2
replies
3.5k
views
pheatmap troubles...!!
gsva
R
Rstudio
pheatmap
heatmap
updated 4.6 years ago by
gglim
▴ 220 • written 4.6 years ago by
Joori
• 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
juanjo75es
▴ 130 • written 4.6 years ago by
marongiu.luigi
▴ 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
lieven.sterck
16k • written 4.6 years ago by
anasofiamoreira94
▴ 80
2
votes
1
reply
1.2k
views
IGH on Ensembl
Ensembl
IGH
updated 4.6 years ago by
Emily
24k • written 4.6 years ago by
chaochao
▴ 20
1
vote
2
replies
1.9k
views
SynChro input files
SynChro
updated 2.7 years ago by
Ram
45k • written 6.8 years ago by
jmah
▴ 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
ellimilial
▴ 20 • written 4.8 years ago by
gjespitia
▴ 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
Ram
45k • written 4.6 years ago by
Apex92
▴ 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
zx8754
12k • written 4.6 years ago by
Sebastian Margherita
• 0
0
votes
1
reply
1.1k
views
Export ensembl efetch in comma-delimited format
format
efetch
ensembl
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
marongiu.luigi
▴ 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
GenoMax
154k • written 4.6 years ago by
salman_96
▴ 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
minyakharum02
• 0 • written 8.7 years ago by
Dave
▴ 110
0
votes
1
reply
964
views
Chosing a phylogenetic tree construction method
tree
phylogenetic
method
updated 4.6 years ago by
Colaptes
▴ 120 • written 4.6 years ago by
A_heath
▴ 180
0
votes
1
reply
1.7k
views
error in snakemake
gatk
snakemake
updated 4.6 years ago by
cpad0112
21k • written 4.6 years ago by
kamanovae
▴ 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
ATpoint
90k • written 5.1 years ago by
rodolfo.peacewalker
▴ 390
1
vote
2
replies
1.1k
views
bedtools error
bedtools
bash
updated 4.6 years ago by
ATpoint
90k • written 4.6 years ago by
rjqmantaring
• 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
Zhilong Jia
★ 2.2k • written 4.6 years ago by
MaxF
▴ 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
Ram
45k • written 9.2 years ago by
ankur.ganveer
▴ 20
1
vote
5
replies
2.5k
views
hisat2 error
hpc
hisat2
updated 4.6 years ago by
Ram
45k • written 4.6 years ago by
loicborcard01
▴ 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
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strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
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Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
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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.
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Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
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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
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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…
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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
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Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
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by
Kent
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Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
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Luca Arbore
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Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets
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In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
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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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