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Limit : this week
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119 results • Page
1 of 3
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Views
Votes
Replies
7
votes
12
replies
812
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA
integrated
ATAC-seq
updated 3 days ago by
Sasha
▴ 180 • written 9 days ago by
Chris
▴ 100
4
votes
6
replies
509
views
How to pass from DNA to AA fasta
genetics
updated 5 days ago by
Buffo
★ 2.2k • written 8 days ago by
Anderson Stiward
• 0
4
votes
8
replies
502
views
Error while running nf-core/rnaseq pipeline
nf-core
RNA-seq
4 days ago by
eesha28112001
• 0
3
votes
5
replies
322
views
Uniprot API access to download .pdb files
PDB
API
Python
Uniprot
3 days ago by
jdrohan
• 0
3
votes
4
replies
1.3k
views
fastPHASE -F provided to estimate haplotype frequencies, but no freqs in output
genomics
phasing
fastPHASE
updated 5 days ago by
Ram
39k • written 5.2 years ago by
lakemonster
▴ 10
3
votes
6
replies
498
views
Convert Nanopore Fast5 files to Fasta format
fast5
fasta
Nanopore
3 days ago by
Sowmya Pulapet
▴ 30
3
votes
8
replies
1.7k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 2 days ago by
Ram
39k • written 4.6 years ago by
nagendranp1991
• 0
3
votes
1
reply
253
views
chromosome location to gene name and aa change
variant-annotation
6 days ago by
Zi
• 0
2
votes
2
replies
765
views
Final year project query
project
updated 2 days ago by
Ram
39k • written 4.5 years ago by
talhar123456
• 0
2
votes
6
replies
516
views
how to make a venn plot with data frame in R
plot
R
Venn
6 days ago by
satva72
• 0
2
votes
3
replies
236
views
Using RNA-seq to detect pathogen sequences in host tissue
RNA-seq
3 days ago by
erik.burchard
▴ 10
2
votes
2
replies
181
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 1 day ago by
Istvan Albert
98k • written 1 day ago by
antoine.fauchois92
▴ 20
2
votes
3
replies
859
views
Freebayes command stopped due to lack of space
freebayes
SNP-calling
updated 3 days ago by
Ram
39k • written 5.0 years ago by
amcheroo
• 0
2
votes
7
replies
1.5k
views
Technology Stack of NCBI (Genbank, GEO, etc.)
sequence
ncbi
gene
genbank
updated 5 days ago by
Ram
39k • written 5.2 years ago by
navela78
▴ 70
2
votes
6
replies
359
views
Find data-based Gene_IDs for unknown gene_IDs in gtf.file
RNA-SEQ
annotation
GO-term
6 days ago by
Pegasus
▴ 90
1
vote
0
replies
1.2k
views
sequence alignment using edlib c++ library
cpp
alignment
updated 5 days ago by
Ram
39k • written 4.8 years ago by
BDK_compbio
▴ 130
1
vote
2
replies
185
views
INSTALLING DEseq2 via conda
seq
conda
RNA
Dseq2
updated 1 day ago by
colindaven
4.8k • written 2 days ago by
Fizzah
▴ 20
1
vote
4
replies
2.5k
views
DBD::mysql::st execute failed: The table 'InplgOrthoInplg
orthomcl
ortho
ubuntu
mysql
updated 3 days ago by
Ram
39k • written 5.0 years ago by
wocana
▴ 20
1
vote
1
reply
144
views
Import Pymol into Python Script
Pymol
python
updated 2 days ago by
Wayne
★ 1.8k • written 2 days ago by
jdrohan
• 0
1
vote
0
replies
1.2k
views
Align two single cell experiments
R
single-cell
updated 2 days ago by
Ram
39k • written 4.5 years ago by
elb
▴ 230
1
vote
5
replies
1.3k
views
WGCNA Co-expression network analysis on cuffdiff output
wgcna
cuffdiff
updated 3 days ago by
Ram
39k • written 4.7 years ago by
sbb
▴ 10
1
vote
1
reply
1.3k
views
Can HISAT2 be invoked in bash shell, and can it be fed variables or names with wildcards as inputs?
Bash
Shell
HISAT2
updated 1 day ago by
Ram
39k • written 4.3 years ago by
RNAseqer
▴ 240
1
vote
4
replies
956
views
Simulate the sequence data
next-gen-sequencing
genetics
updated 5 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
1
vote
1
reply
636
views
How to determine seq technology used in genome assembly?
sequencing
updated 5 days ago by
Ram
39k • written 5.1 years ago by
maximilian.mayerhofer
▴ 30
1
vote
5
replies
491
views
kraken on nt library
kraken
nt
4 days ago by
Francois Piumi
▴ 30
1
vote
5
replies
263
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
updated 1 day ago by
GenoMax
129k • written 1 day ago by
DanielEB_fisk
• 0
1
vote
2
replies
228
views
highlight regions in a dot-plot?
figure
dotplot
alignment
synteny
2 days ago by
Buffo
★ 2.2k
1
vote
3
replies
322
views
Retrieve Promoter Sequences by GeneID
GeneID
by
Sequences
Retrieve
Promoter
updated 4 days ago by
lieven.sterck
14k • written 4 weeks ago by
alessandro.alma00
• 0
1
vote
1
reply
181
views
merging structural variants from various callers into one vcf file (long read sequencing)
vcf
longread
updated 4 days ago by
LChart
2.6k • written 4 days ago by
Shaghayegh
▴ 20
1
vote
3
replies
288
views
Pre-processing for Agilent microarray data?
affymetrix
microarray
gene
agilent
rna
updated 2 days ago by
ATpoint
72k • written 4 days ago by
survive
• 0
1
vote
3
replies
329
views
Variant calling analysis
vcf
variant-calling
wgs
updated 5 days ago by
Medhat
9.6k • written 6 days ago by
namck
• 0
1
vote
2
replies
261
views
Identifying/Annotating Enhancers
enhancer
R
ENCODE
bedtools
updated 3 days ago by
ATpoint
72k • written 4 days ago by
cthangav
▴ 40
1
vote
2
replies
2.0k
views
Error in Adding 1000Genomes Ancestral Allele info: Using VCF tools fill-aa
vcftools
samtools
faidx
tabix
1000Genomes
updated 5 days ago by
barslmn
★ 1.5k • written 5.6 years ago by
shrutishreyajha
▴ 10
1
vote
0
replies
167
views
How to assess which cell population is most affected by treatmant in single cell rna seq data?
transcriptomics
single-cell
RNA
DEG
1 day ago by
abbas89
▴ 10
1
vote
2
replies
160
views
Abyss taking a Long time to run
abyss
assembly
genome
fastq
1 day ago by
Maliha
▴ 20
1
vote
10
replies
2.5k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 1 day ago by
Ram
39k • written 4.2 years ago by
Kumar
▴ 100
1
vote
1
reply
984
views
cfDNA target seq vs. cfDNA WES
cfDNA
updated 3 days ago by
Ram
39k • written 4.9 years ago by
genetic
▴ 40
1
vote
14
replies
2.8k
views
How to convert Haplotypes file to PLINK format data
R
plink
updated 4 days ago by
Ram
39k • written 5.0 years ago by
bha
▴ 80
1
vote
2
replies
202
views
Create clustered bar chart in R
R
ggplot
visualization
1 day ago by
Prangan
▴ 20
1
vote
3
replies
751
views
Stratify phylogeny based on variables - e.g. which ST are represented by high % males
phylogeny
statistics
updated 1 day ago by
Ram
39k • written 4.3 years ago by
kalfsnes
▴ 10
1
vote
3
replies
346
views
how to do an "reverse" oncoplot in maftools
maftools
Rstudio
updated 4 days ago by
Ram
39k • written 8 days ago by
JULIA HELENA
• 0
0
votes
1
reply
133
views
making metadata file for differential gene expression analysis
RNAseq
updated 2 days ago by
Basti
★ 1.5k • written 2 days ago by
Sara
▴ 220
0
votes
1
reply
152
views
Variant Annotation
Variant-Annotation
VCF
R
updated 1 day ago by
Ram
39k • written 1 day ago by
Chethana
• 0
0
votes
16
replies
3.1k
views
Gff to genbank - feature is missing
DNA
augustus
gff3
genbank
updated 4 days ago by
Ram
39k • written 5.0 years ago by
rororo
• 0
0
votes
1
reply
931
views
Questions about assembly of large metagenomics dataset
assembly
metagenomics
megahit
updated 2 days ago by
Ram
39k • written 4.5 years ago by
zorrilla
• 0
0
votes
4
replies
483
views
From VCF to BEAGLE format with multiple chromosomes
vcf
vcftools
beagle
gvcf
3 days ago by
Begonia_pavonina
▴ 100
0
votes
2
replies
2.5k
views
How to get Haplotype file from PLINK format data
SNP
PLINK
updated 5 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
0
votes
1
reply
142
views
Samtools index and sambamba-depth error?
linux
samtools
indexing
sambamba
updated 3 days ago by
Pierre Lindenbaum
154k • written 3 days ago by
MobiusT
▴ 10
0
votes
2
replies
348
views
Trouble annotating heatmap with pheatmap. Error in annotation_col[colnames(mat), , drop = F] : subscript out of bounds
pheatmap
4 days ago by
oleksandra.kalnytska
• 0
0
votes
2
replies
173
views
Repbase database and transposon sequence
TE
TSD
TIRs
Tpase
1 day ago by
manaswiniparija3
▴ 10
119 results • Page
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Recent Votes
Answer: IGV displays genomic coordinates in a 1-based system or 0-based?
RNAseq expression data log2 transformed has negative values.
Samtools: "Too Many Open Files"
Filtering bad quality probes in illumina microarray data
gene filtering for agilent microarray using Limma
A: Identification Of Significant Differences Between Phylogentic Trees Using Distan
A: How to filter vcf file on minimum genotype depth and quality for each sample
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Answer: Counting intronic reads in bulk RNA-seq
by
swbarnes2
13k
Are you sure this is appropriate for bulk RNASeq? I thought intronic reads for single cell were only counted in nuclear preps.
Answer: Single cell chemistry
by
swbarnes2
13k
Are you sure these samples are 10x? How likey is it that the sequencing group messed up and ran the samples wrongly?
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Vincent Laufer
★ 2.8k
are they distinct transcript IDs but the same gene ID? can you provide any additional context?
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
Dhatri Badri
• 0
that didn't work either
Answer: Why are some WES VCFs larger than others?
by
Vincent Laufer
★ 2.8k
Hi @kermit and prash (and others)! Nice discussion. I wanted to offer some **biological rationales** in addition to the technical reasons …
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
WouterDeCoster
47k
There is no `:` after `rule fastqc`
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
Dhatri Badri
• 0
sorry that was a typo while i was copying my code! I still get the same error
Comment: too many zeros in 16S rRNA amplicon sequencing data
by
andres.firrincieli
3.3k
You have too many ASV (40k) and I think this is a problem related to the denoising (DADA2) of NovaSeq 6000 sequencing data. Maybe this post…
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
Pierre Lindenbaum
154k
> fastq.gz". what is the dot after `fastq.gz" ` ?
Comment: DownsampleSam
by
Pierre Lindenbaum
154k
1) I think this is just a warning 2) there must be another error displayed 3) look at samtools view --subsample 4) don't use loops but use…
Comment: ABySS genome assembler
by
npavliukovec
• 0
Hello, yes, I tried it, but I have to do my home work on university's remote computer, unfortunatelly I go an error, when I try to use abys…
Comment: desgin a primer for CDS
by
yuxiang
• 0
how can you know the primer is not bind to other gene site? how can you desgin an experiment? I use the FISH to identify the gene, how abo…
Comment: desgin a primer for CDS
by
yuxiang
• 0
sorry for my late reply, I am a student, my profossor ask me to dsgin a primer for the specific cDNA, I have solved now, thanks for your re…
Comment: vg: Mapping fewer reads to a genome graph than a linear reference
by
samuel.a.odonnell
▴ 470
In this case filtering for quality might help correct for this overattributing feature?
Comment: ABySS genome assembler
by
GenoMax
129k
Did you see this guidance from ABySS manual: https://github.com/bcgsc/abyss#optimizing-the-parameters-k-and-kc
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