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1
vote
8
replies
367
views
syntax errors when running part3 all-against-all
oma
3 hours ago by Sofia • 0
0
votes
0
replies
51
views
How to get BEAGLE files from VCF with angsd?
angsd vcf populationgenetics beagle pcangsd
5 hours ago by Begonia_pavonina ▴ 90
0
votes
0
replies
71
views
How to find p-values for annotated methylated regions using methylkit and genomation
NGS bioinformatics pvalue annotation methylationarray
6 hours ago by Saransh • 0
3
votes
3
replies
246
views
Snakemake workflow for trimmomatic
snakemake
updated 3 hours ago by 127k • written 1 day ago by • 0
0
votes
0
replies
143
views
Job: PhD project: Analysis Of Genomics And Epigenomics Data In Mice And Humans To Clarify The Identity Of Plasmacytoid Dendritic Cells And Their Physiolog…
bioinformatics dendritic system cells immune multiomics
12 hours ago by aitor.gonzalez ▴ 30
1
vote
1
reply
161
views
My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
R ENSEMBL DESeq2
updated 17 hours ago by 127k • written 18 hours ago by • 0
0
votes
0
replies
100
views
Which ATAC-seq SAM/BAM fields are required for bigwig generation by deeptools bamCoverage?
SAM BAM Fields bamCoverage deeptools
18 hours ago by Deep • 0
0
votes
2
replies
175
views
Gene duplicate
monocle3
updated 20 hours ago by 71k • written 21 hours ago by • 0
0
votes
0
replies
117
views
HiC analysis in R
R HiC
updated 21 hours ago by 38k • written 22 hours ago by • 0
0
votes
1
reply
169
views
TCGA-BRCA tissue and RNAseq problem
NIH RNAseq GDC TCGA-BRCA
updated 7 hours ago by ▴ 10 • written 1 day ago by • 0
0
votes
1
reply
165
views
R package for functional enrichment and depletion analysis
enrichment depletion
updated 21 hours ago by 11k • written 1 day ago by ★ 1.3k
2
votes
2
replies
172
views
How to remove duplicate reads after ONT basecalling from fastq.gz files
fastq
22 hours ago by Darrenjdd • 0
0
votes
2
replies
154
views
Gene family classification using RNA-seq data
RNA_seq gene_expression gene_family
6 hours ago by Dion • 0
0
votes
3
replies
216
views
How to deal with the probe id mapping to multiple gene ids?
match microarray affymetrix probe gene
13 hours ago by dare_devil ★ 1.7k
3
votes
3
replies
228
views
PTM-aware protein folding / docking
docking protein-structure folding
updated 23 hours ago by ★ 23k • written 3 days ago by 2.2k
0
votes
2
replies
180
views
Quality control of Chip-seq data (NRF and PCB)
control library quality PCB Chip-seq NRF
3 hours ago by michelafrancesconi9 • 0
1
vote
4
replies
332
views
Snakemake doesn't recognize output files even though they are created
python Snakemake
19 hours ago by DdogBoss • 0
0
votes
0
replies
106
views
Nucleotide substitution model and neighbor-joining tree
phylogeny substitution mega neighbor-joining modeltest
3 hours ago by poecile.pal ▴ 50
1
vote
4
replies
408
views
SKAT in R
pvalue skat snp
7 hours ago by Eliza ▴ 20
1
vote
7
replies
520
views
Dependent p values
pvalue snp Gene
8 hours ago by Eliza ▴ 20
8
votes
8
replies
1.3k
views
Tool: pyCirclize - Circular visualization in Python
visualization circos matplotlib genome python
updated 4 hours ago by ▴ 40 • written 3 months ago by ▴ 110
0
votes
2
replies
306
views
LDSC correlation calculate confidence intervals
correlation intervals confidence genetic LDSC
19 hours ago by YL ▴ 10
1
vote
3
replies
1.5k
views
How to get aligned protein data from DNA sequences.
protein alignment DNA
updated 21 hours ago by 38k • written 7.4 years ago by • 0
7
votes
4
replies
2.8k
views
Why Chip-seq data cross correlation plot has fragment_lenth cross correlation peak and read-length peaks
chip-seq quality-control cross correlation
updated 22 hours ago by • 0 • written 3.8 years ago by ▴ 110
5
votes
4
replies
2.2k
views
strand specificity of TFBS
motif transcription-factor TFBS
updated 23 hours ago by 38k • written 7.4 years ago by ▴ 80
4
votes
8
replies
6.4k
views
SNPs located in promoter region. OR exon, intron, 5'UTR, 3'UTR
SNP
updated 21 hours ago by 38k • written 7.3 years ago by • 0
31
votes
34
replies
5.7k
views
11 follow
Forum: pros- and cons- : programming skills vs. GUI
programming lecture
updated 21 hours ago by 38k • written 7.3 years ago by ★ 4.6k
6
votes
5
replies
2.1k
views
Forum: Bioinformatics course good for microbiology student or not?
career
updated 21 hours ago by 38k • written 7.3 years ago by ▴ 10
0
votes
0
replies
1.9k
views
Job: PhD Studentships @ University of Glasgow [International students can also apply]
phd
updated 21 hours ago by 38k • written 7.3 years ago by ★ 1.8k
0
votes
0
replies
1.3k
views
Job: PhD Studentship in bioinformatics
next-gen RNA-Seq
updated 21 hours ago by 38k • written 7.3 years ago by • 0
3
votes
9
replies
2.9k
views
Need recommendation for a virtual machine or linux cluster for ngs analysis
ngs
updated 21 hours ago by 38k • written 7.4 years ago by ▴ 220
1
vote
7
replies
2.4k
views
Forum: Bioinformatics & Virology or Immunology.
immunology virology
updated 21 hours ago by 38k • written 7.4 years ago by • 0
1
vote
1
reply
4.2k
views
How to Determine the Most Conserved Sequence from BLAST Result?
blast sequence-alignment
updated 21 hours ago by 38k • written 7.4 years ago by ▴ 30
3
votes
4
replies
4.8k
views
How to visualize sequence quality control distribution
sequence Fastq R
updated 21 hours ago by 38k • written 7.4 years ago by ▴ 30
2
votes
1
reply
1.5k
views
ensemble illumina tissues aligned rnaSeq
alignment RNA-Seq gene ISOFORM
updated 21 hours ago by 38k • written 7.4 years ago by ▴ 10
79
votes
34
replies
7.7k
views
15 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship career
updated 21 hours ago by 38k • written 7.4 years ago by ▴ 650
0
votes
1
reply
1.4k
views
TMREC(Transcription factor and miRNA regulatory cascade in human diseases) database
transcription-factors database
updated 21 hours ago by 38k • written 7.4 years ago by • 0
4
votes
4
replies
2.1k
views
What protein structure do human proteins refer to?
protein protein-structure
updated 23 hours ago by 38k • written 7.4 years ago by ▴ 10
8
votes
4
replies
1.7k
views
Forum: Tutorials for families of cancer patients
diagnosis cancer
updated 23 hours ago by 38k • written 7.4 years ago by ▴ 70
0
votes
2
replies
3.4k
views
Interproscan nucleotide sequence scanning
software-error sequence
updated 23 hours ago by 38k • written 7.4 years ago by ▴ 230
40 results • Page 1 of 1
Recent Votes
Answer: Snakemake workflow for trimmomatic
C: Adjust for covariates
Comment: syntax errors when running part3 all-against-all
Picard LiftOver rejecting all Variants
Comment: pyCirclize - Circular visualization in Python
Answer: What is the major problem with this pipeline of SNPs analysis?
pyCirclize - Circular visualization in Python
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Recent Replies
Comment: Snakemake workflow for trimmomatic by GenoMax 127k
Please accept this answer (green check mark) to provide closure to this thread.
Comment: syntax errors when running part3 all-against-all by Sofia • 0
When I started with the gz all-vs-all files for CHICK and ANOCA and started oma, everything ran fine, I got output. Then, in the same direc…
Comment: Quality control of Chip-seq data (NRF and PCB) by michelafrancesconi9 • 0
Can you explain me better? Because for the NRF I do : a) samtools view -c .bam b)samtools view -c -F 260 .bam then b/a and as a bam fi…
Comment: pyCirclize - Circular visualization in Python by karenkvn ▴ 40
Thank you for responding so quickly - this works perfectly!
Comment: pyCirclize - Circular visualization in Python by moshi ▴ 110
Please install Biopython with v1.80 or higher. If biopython>=1.80, there should be no errors.
Comment: Gene family classification using RNA-seq data by Dion • 0
well, I have been given the task to retrieve gene family/categorization. I found sveral papers on family classification, but no actual pack…
Comment: pyCirclize - Circular visualization in Python by karenkvn ▴ 40
Thank you for this wonderful programme! I am plotting a bacterial chromosome and find that when I plot the NC_000913 chromosome using the e…
Comment: SKAT in R by Eliza ▴ 20
@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
Comment: TCGA-BRCA tissue and RNAseq problem by pinheirofabiano ▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Comment: Snakemake workflow for trimmomatic by antoine.fauchois92 • 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values by Eliza ▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids? by GenoMax 127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL by rpolicastro 11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
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