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52 results • Page
1 of 2
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Rank
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0
votes
0
replies
1
view
Homer annotatePeaks for enrichment analysis
annotatePeaks
homer
DMR
methylation
just now by
Joana
• 0
0
votes
0
replies
5
views
Snakemake vs Nextflow Upcoming bioinformatics Project
Bioinformatics
Programming
Masters
8 minutes ago by
rackbersingh
• 0
0
votes
0
replies
23
views
Seurat analysis without ribosomal genes
single-cell
transcriptomics
seurat
33 minutes ago by
firestar
★ 1.5k
0
votes
2
replies
33
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
15 minutes ago by
TJay
• 0
0
votes
0
replies
18
views
Add HI:i:<n> tag to a BAM file
SAM
hisat2
STAR
tag
BAM
1 hour ago by
predeus
★ 1.8k
0
votes
0
replies
28
views
Quality control of the X-chromosome for use in a GWAS using REGENIE
REGENIE
GWAS
LMM
chromosome-X
quality-control
1 hour ago by
ucbtep
▴ 20
2
votes
5
replies
91
views
GATK GenotypeGVCFs explain
calling
gatk
variant
GenotypeGVCFs
updated 1 hour ago by
Pierre Lindenbaum
153k • written 3 hours ago by
Sarah
▴ 30
0
votes
0
replies
61
views
Dnaplotter
Artemis
4 hours ago by
prs
• 0
1
vote
1
reply
98
views
How to create GO Bar Plot using data obtained from DAVID Functional Enrichment Analysis?
Plot
DAVID
R
updated 3 hours ago by
Basti
★ 1.4k • written 5 hours ago by
Stefanus C.B.
• 0
0
votes
1
reply
101
views
mrbayes segmentation fault
mrbayes
segmentation
fault
updated 5 hours ago by
Mensur Dlakic
★ 23k • written 8 hours ago by
dgrace999
• 0
0
votes
0
replies
72
views
Obtain the GenomicRanges from segmented CNA data and the corresponding TSS for EnrichedPlot
TSS
GRanges
EnrichedPlot
promoters
GenomicRanges
9 hours ago by
melissachuaphd
• 0
0
votes
0
replies
76
views
ChIPseq w/ polyploid genome : Xenopus laevis
chipseq
alignment
xenopus
ploidy
13 hours ago by
William
▴ 10
0
votes
0
replies
101
views
Differential (pathways) expression testing using linear model packages in R (Limma & GSVA)
GSVA
limma
R
13 hours ago by
Tadeoye
▴ 30
0
votes
0
replies
93
views
How to quantify the expression of CD45 isoforms from bulk RNA-seq data
isoforms
Salmon
RNA-seq
CD45
14 hours ago by
eager_underdog
• 0
0
votes
5
replies
207
views
How can I determine the number of detected genes and detected transcripts/isoforms in a BAM file + GTF file?
rnaseq
scRNA-seq
single-cell
genomics
ngs
updated 20 minutes ago by
GenoMax
126k • written 14 hours ago by
O.rka
▴ 650
0
votes
2
replies
153
views
Processing fastqs generated by inDrop protocol
single-cell
rna-seq
indrop
updated 13 hours ago by
Ram
38k • written 15 hours ago by
bobbybobbobbo
• 0
1
vote
3
replies
198
views
How to extract/find the actual names of the gene_IDs if they are not fully presented in gtf.file, and link them to the Count.matrix
featureCounts
gtf
RNA-Seq
updated 14 hours ago by
GenoMax
126k • written 16 hours ago by
Pegasus
▴ 80
0
votes
1
reply
118
views
Circos plot
circos
updated 3 hours ago by
Fabio Marroni
★ 3.0k • written 16 hours ago by
prs
• 0
0
votes
1
reply
97
views
mpileup2sync
mpileup2sync
population2
updated 16 hours ago by
Ram
38k • written 17 hours ago by
Hayler Edu
▴ 30
0
votes
0
replies
74
views
Number of gigabases necesary for Iso-seq-PacBio
Iso-seq
RNA-Seq
Alternative-Splicing
PacBio
updated 17 hours ago by
Ram
38k • written 18 hours ago by
Jesús M
• 0
0
votes
2
replies
127
views
Problem with blasting UNMAPPED RNA-seq paired end reads in Jaculus jaculus
RNAseq
jaculus
unmapped
reads
18 hours ago by
barbarainb
• 0
0
votes
0
replies
59
views
PGx question regarding RSIDs with more than one variant associated with it
pharmacogenomics
rsid
pgx
19 hours ago by
Roy
▴ 10
0
votes
0
replies
85
views
Converting Abricate output (.tsv) to gff3 format
gff3
convert
tsv
Abricate
22 hours ago by
ghataksnd
▴ 10
0
votes
0
replies
94
views
samtools mpileup - bases string explanation
samtools
mpileup
23 hours ago by
igorm
▴ 20
0
votes
3
replies
207
views
Problem in converting SAM to BAM file by DROP SEQ
SAMtoBAM
updated 16 hours ago by
Ram
38k • written 1 day ago by
VANSHIKA
• 0
0
votes
1
reply
178
views
Error while running Virusfinder
Virusfinder
updated 17 hours ago by
Ram
38k • written 1 day ago by
DC
• 0
1
vote
3
replies
249
views
FeatureCounts >edgeR > GO
RNA-SEQ
updated 3 hours ago by
Basti
★ 1.4k • written 1 day ago by
Pegasus
▴ 80
0
votes
1
reply
210
views
Circos plot using vcf : Mutect2 MultiSample VCF out file
Mutect2
vcf
updated 16 hours ago by
Ram
38k • written 2 days ago by
m. bioinfo
• 0
0
votes
2
replies
290
views
Post-Imputation QC Problem
Imputation
18 hours ago by
Jesse
• 0
6
votes
11
replies
652
views
Calculate RPKM
RPKM
6 hours ago by
Chris
▴ 70
0
votes
0
replies
178
views
Enrichment map in python/ Pathway network by using python
network
pathway-enrichment
interaction
updated 16 hours ago by
Ram
38k • written 6 weeks ago by
sonsunjirachote
• 0
0
votes
1
reply
189
views
How to obtain unmapped reads from the paired end samples using hisat2
fastq
hisat2
updated 16 hours ago by
Ram
38k • written 8 weeks ago by
otieno43
• 0
3
votes
4
replies
471
views
Changing Temporary File Location for Local BLASTP to nr Database
protein
blast
nr
updated 16 hours ago by
Ram
38k • written 9 weeks ago by
katieostrouchov
▴ 20
0
votes
2
replies
308
views
When do the PCR Bottlenecking Coefficient
PCR
bam
chip-seq
updated 16 hours ago by
Ram
38k • written 9 weeks ago by
michelafrancesconi9
• 0
0
votes
4
replies
580
views
I want to merge gene sequences in fasta to create one genome from all cds region.
fasta
linux
genome
updated 16 hours ago by
Ram
38k • written 10 weeks ago by
iankeetkumar
• 0
0
votes
2
replies
291
views
bed file question! [extract read numbers from bed file]
BED
updated 15 hours ago by
Ram
38k • written 4 months ago by
Jjbox
▴ 40
0
votes
1
reply
322
views
Translating a Fasta File
fasta
translation
updated 15 hours ago by
Ram
38k • written 4 months ago by
Hb
• 0
0
votes
0
replies
165
views
Count read numbers of splice junctions from BED file
BED
updated 15 hours ago by
Ram
38k • written 4 months ago by
Jjbox
▴ 40
0
votes
0
replies
230
views
What can I do after enrichment of expression microarray?
Agilent
array
DEG
16 hours ago by
Di Wu
• 0
1
vote
1
reply
174
views
Problem in generating the BAM files using STAR
BAM
STAR
updated 15 hours ago by
Ram
38k • written 6 months ago by
boomathi.91
• 0
0
votes
2
replies
296
views
Trouble using Human_GeCKOv2_Library_combine.csv to run MAGeCK
nontarget-sgrna
MAGeCK
updated 16 hours ago by
Ram
38k • written 8 months ago by
teresa
• 0
0
votes
0
replies
293
views
R package PopGenome : error with introgression.stats function
PopGenome
R
updated 16 hours ago by
Ram
38k • written 10 months ago by
fabien-reygiraud
• 0
0
votes
0
replies
163
views
Estimating gene flow in non-structured populations
TreeMix
SNP
updated 16 hours ago by
Ram
38k • written 11 months ago by
Camila Martínez
▴ 30
1
vote
5
replies
1.2k
views
Star index generation - 'std::bad_alloc' error
STAR
updated 14 hours ago by
Ram
38k • written 2.2 years ago by
aranyak111
• 0
1
vote
7
replies
1.7k
views
Platypus variantcaller.c:16971 errpr
platypus
updated 16 hours ago by
Ram
38k • written 4.2 years ago by
nuketbilgen
▴ 40
1
vote
1
reply
1.5k
views
Error: Sieve v.2.2 (Label-free mass spectrometery differential analysis) - Index bounds outside the array
LFQ
Mass-Spectrometry
LC-MS-MS
updated 16 hours ago by
Ram
38k • written 4.6 years ago by
Ramaraj K
• 0
1
vote
1
reply
1.9k
views
Updated list of bioinformatics jobs sites
career
updated 14 hours ago by
Ram
38k • written 7.9 years ago by
Pappu
★ 2.1k
0
votes
0
replies
1.5k
views
xcolor.sty package problem
bcftools
xcolor.sty
updated 16 hours ago by
Ram
38k • written 6.7 years ago by
viswanathrana29
▴ 20
0
votes
1
reply
2.1k
views
How would sequence overrepresentation and duplication level affect the quality of a De Novo transcriptome assembly?
next-gen
Assembly
Trinity
RNA-Seq
updated 14 hours ago by
Ram
38k • written 7.9 years ago by
guillermo.ponz.segrelles
▴ 20
6
votes
9
replies
4.7k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 14 hours ago by
Ram
38k • written 7.9 years ago by
gaurav.singh
▴ 10
52 results • Page
1 of 2
Recent Votes
Answer: Extract Sub_Tree From Big Phylogeny
How to pair TCGA bam files with no properly paired reads?
How to pair TCGA bam files with no properly paired reads?
Answer: How to implement this two-stage one-to-many workflow using WDL?
Answer: How to implement this two-stage one-to-many workflow using WDL?
Answer: How to implement this two-stage one-to-many workflow using WDL?
Creating workflows with snakemake and conda
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Popular Question
to
TJay
• 0
Scholar
to
GenoMax
126k
Popular Question
to
predeus
★ 1.8k
Popular Question
to
eennadi
▴ 20
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shenwei356
7.9k
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Zhilong Jia
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LChart
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Recent Replies
Comment: Plot heatmap using row_splitting but splitting should based on a column in data
by
TJay
• 0
Any guidance to make annotation object?
Comment: Plot heatmap using row_splitting but splitting should based on a column in data
by
rpolicastro
11k
Instead of splitting your dataset you want to make an annotation object via `rowAnnotation` and then pass it to the `left_annotation` argum…
Comment: How can I determine the number of detected genes and detected transcripts/isofor
by
GenoMax
126k
If this is single cell data then this is likely because of the 3' end detection bias. In general you are also detecting less genes because …
Comment: gene filtering for agilent microarray using Limma
by
Di Wu
• 0
Dear Prof. Kevin Blighe, many thanks for your quick reply. About the `correlation` value, I used the following code for getting the value. …
Comment: GATK GenotypeGVCFs explain
by
Pierre Lindenbaum
153k
https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists
Comment: GATK GenotypeGVCFs explain
by
Sarah
▴ 30
thank you
Comment: GATK GenotypeGVCFs explain
by
raphael.B
▴ 270
It limits the operation to some genomic regions given as parameter
Comment: GATK GenotypeGVCFs explain
by
Sarah
▴ 30
what does the option L
Comment: GATK GenotypeGVCFs explain
by
Pierre Lindenbaum
153k
GenotypeGVCFs takes a set of GVCF files called with HaplotyperCaler and output a VCF file.
Answer: TCGA Methylation Data and Gene Mapping
by
Basti
★ 1.4k
CpGs may be annotated to more than >1 gene simply because gene regions overlap on the genome. If you want to associate each gene to a me…
Comment: Circos plot
by
Fabio Marroni
★ 3.0k
Please give a look to [this post][1] for increasing the probability to get an answer. If I may add some needed info: 1. What exactly do y…
Comment: Trying to install Roary with Conda results in error message
by
tobiwan
▴ 10
Wow, thank you so much for your explanation! My conda channel is indeed set to strict priority. Should packages with different dependencie…
Comment: FeatureCounts >edgeR > GO
by
Basti
★ 1.4k
You can use BioMart to convert your "gene-IDs" to gene symbols, but you need to specify from which database your gene identifiers come from
Comment: How to create GO Bar Plot using data obtained from DAVID Functional Enrichment A
by
Basti
★ 1.4k
If you search "DAVID dotplot" on this forum, you have many answers to your question. Note that you can also perform DAVID Functional Enrich…
Answer: How to implement this two-stage one-to-many workflow using WDL?
by
Pierre Lindenbaum
153k
nottested, something like: ``` version 1.0 workflow BIOSTAR { call FIRST { } scatter (F in FIRST.each_F)…
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