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Limit : this week
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185 results • Page
2 of 4
Sort: replies
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Views
Votes
Replies
2
votes
4
replies
311
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
5 days ago by
Esraa
• 0
3
votes
4
replies
414
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Pierre Lindenbaum
161k
2
votes
4
replies
277
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 4 days ago by
yura.grabovska
▴ 90 • written 4 days ago by
ev97
▴ 20
0
votes
4
replies
269
views
Galaxy StringTie error
stringtie
galaxy
6 days ago by
trkfs
• 0
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 6 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
0
votes
4
replies
138
views
Why most genes have high padj values
deg
padj
bulkRNA
4 hours ago by
mnx0723
• 0
0
votes
4
replies
286
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
2 days ago by
mavy
▴ 10
1
vote
3
replies
209
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 4 days ago by
shpak.max
▴ 50
1
vote
3
replies
453
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
6 days ago by
kalavattam
▴ 190
0
votes
3
replies
374
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
6 days ago by
mropri
▴ 150
0
votes
3
replies
200
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 6 days ago by
Ram
43k • written 7 days ago by
yau
• 0
3
votes
3
replies
298
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 6 days ago by
Ram
43k • written 20 days ago by
Adyasha
• 0
3
votes
3
replies
369
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 6 days ago by
Mathew
▴ 140 • written 9 days ago by
Christopher
• 0
0
votes
3
replies
359
views
Snakemake wrapper issue
fastqc
snakemake
updated 6 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
215
views
How to access GWAVA software of data
GWAVA
updated 6 days ago by
GenoMax
142k • written 6 days ago by
nonaddldy
▴ 10
0
votes
3
replies
222
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 6 days ago by
GenoMax
142k • written 6 days ago by
RNAseqer
▴ 270
2
votes
3
replies
291
views
Finding variants within a subset of a BAM file
variant
calling
5 days ago by
ramiro.barrantes
• 0
0
votes
3
replies
271
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 5 days ago by
noodle
▴ 580 • written 5 days ago by
doramora
▴ 10
2
votes
3
replies
220
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 5 days ago by
Ram
43k • written 5 days ago by
Prawesh
• 0
0
votes
3
replies
172
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
5 days ago by
Esraa
• 0
1
vote
3
replies
298
views
Using ggplotly in R
ggplot
ggplotly
updated 4 days ago by
jared.andrews07
★ 16k • written 5 days ago by
jen
▴ 10
3
votes
3
replies
238
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Alexandra
• 0
3
votes
3
replies
251
views
getting exon coordinates
genomics
updated 3 days ago by
Ram
43k • written 4 days ago by
Xbox_27
• 0
1
vote
3
replies
284
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 3 days ago by
GenoMax
142k • written 6 days ago by
ohtang7
▴ 40
1
vote
3
replies
805
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 3 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
1
vote
3
replies
286
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 3 days ago by
Ram
43k • written 5 days ago by
kuttibiotech2009
▴ 30
2
votes
3
replies
258
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 3 days ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
0
votes
3
replies
282
views
Sam file Header problem
Sam
Header
problem
file
updated 3 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
saifulislam99121
• 0
0
votes
3
replies
265
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 8 hours ago by
nd48
▴ 20 • written 3 days ago by
Umer
▴ 50
0
votes
3
replies
193
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 2 hours ago by
GenoMax
142k • written 1 day ago by
KHURRAM SHAHZAD
• 0
0
votes
3
replies
99
views
GATK Structural Variants Pipeline - Steps
SV
VariantCalling
GATK
2 hours ago by
Bioinformatics_begginner
▴ 20
1
vote
2
replies
213
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 5 days ago by
colindaven
6.4k • written 5 days ago by
mbrav005
• 0
1
vote
2
replies
371
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 6 days ago by
Ram
43k • written 7 days ago by
t.fortunato.asquini
• 0
2
votes
2
replies
193
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 3 days ago by
Ram
43k • written 4 days ago by
jsmith120f
• 0
1
vote
2
replies
698
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 1 day ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
0
votes
2
replies
302
views
Traveler with Infernal mapping failed
r2dt
updated 1 day ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
4
votes
2
replies
197
views
Duplicated sequence samtools
bowtie2
samtools
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Moinuddin
• 0
0
votes
2
replies
213
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
12 hours ago by
Luqman
• 0
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 6 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
3
votes
2
replies
289
views
imputation through beagle
panel
beagle
reference
imputation
6 days ago by
analyst
▴ 50
0
votes
2
replies
232
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
4 days ago by
Chen
• 0
2
votes
2
replies
206
views
genome finishing
finishing
genome
updated 4 days ago by
nd48
▴ 20 • written 5 days ago by
trezini
• 0
0
votes
2
replies
250
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
melissachua90
▴ 70
2
votes
2
replies
209
views
Genome Visualization Tools
bacterial
genome
updated 5 days ago by
GenoMax
142k • written 5 days ago by
dlera.lozano
▴ 10
1
vote
2
replies
235
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
3 days ago by
bioinfo
▴ 150
0
votes
2
replies
442
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
6 days ago by
David Langenberger
11k
0
votes
2
replies
243
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 2 days ago by
LauferVA
4.2k • written 2 days ago by
ijarne
• 0
1
vote
2
replies
207
views
Super ehancers
enhancers
just now by
Oburah
• 0
1
vote
2
replies
319
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 17 hours ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
2
replies
239
views
Trimming tool
Trimmer
tool
updated 2 days ago by
ntsopoul
▴ 60 • written 2 days ago by
GeneC
• 0
185 results • Page
2 of 4
Recent Votes
Answer: How to find identical sequences in genome fasta file (by Python or any possible
Merging/Concatenating Vcf Files
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Answer: Ti Tv ratio and their usefulness in exome sequencing
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Answer: How do you generate TMM normalized counts using EdgeR?
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Answer: How to generate an Upset plot in R to plot the shared variants between cell free
by
zx8754
11k
Try this example: library(UpSetR) #example input, 4 samples, 250 variants set.seed(1); d <- data.frame(matrix(sample…
Answer: Illumina methylation EPIC V2 array
by
fu_entomology
▴ 40
We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vign…
Answer: How to find identical sequences in genome fasta file (by Python or any possible
by
GenoMax
142k
> My final purpose are find and remove any identical sequences present in my genome fasta file. You can use `clumpify.sh` from BBMap suite…
Comment: GO analysis: Indicate genes corresponding to the pathway
by
marco.barr
▴ 130
I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
Comment: GATK Structural Variants Pipeline - Steps
by
Bioinformatics_begginner
▴ 20
Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps
by
Pierre Lindenbaum
161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
Comment: GATK Structural Variants Pipeline - Steps
by
DGTool
▴ 20
If it is just the tools that they used which you are looking for, the first link in the overview section of that page leads to the followin…
Comment: GO analysis: p-value range
by
Matthias Zepper
4.6k
It is just a warning that you add a new scale to a ggplot2 plot, that already has an existing one, which will get replaced. Nothing to worr…
Comment: GO analysis: p-value range
by
marco.barr
▴ 130
If you write me the code you used I can help you more
Comment: GO analysis: p-value range
by
sooni
▴ 20
When I run the code, the following message appears: Scale for y is already present. Adding another scale for y, which will replace…
Comment: Why most genes have high padj values
by
mnx0723
• 0
In the case of other samples, the total number of genes is at least 3,000 more than that one, but it seems to be a relatively small number.…
Comment: How to hide label in layout file of MCscan (python version)
by
jinyi
• 0
Command line is as follows: python -m jcvi.graphics.synteny Cs.Cm.i1.blocks Cs_Cm.bed layout2.txt
Comment: Add stats to the plot
by
marco.barr
▴ 130
Thank you, it seems to be clearer. Your Condition already has two factorial levels. You can replace these names in groups 1 and 2. da…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
marco.barr
▴ 130
Hi, I also had the same problem. If you check its github page there have been no releases for many years and these errors cannot be fixed. …
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