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122,217 results • Page
726 of 2445
Sort: Rank
Rank
Views
Votes
Replies
3
votes
6
replies
3.9k
views
Using GNU parallel to speed up merging VCFs with bcftools
vcf
parallel
gwas
bcftools
bash
4.8 years ago by
mfshiller
▴ 20
0
votes
2
replies
1.5k
views
TCGA: How to detect normal and tumor samples in PRAD dataset?
RNA-Seq
gene
updated 4.5 years ago by
Zhenyu Zhang
★ 1.3k • written 4.8 years ago by
carolgalah
• 0
3
votes
3
replies
2.5k
views
bcftools norm resulting in '*' in alternate allele
SNP
bcftools
VCF
exome
updated 15 months ago by
jon.klonowski
▴ 210 • written 4.8 years ago by
prasundutta87
▴ 730
0
votes
6
replies
2.7k
views
Is using WGCNA package for analyzing 12 samples in 3 studies possible?
RNA-Seq
R
WGCNA
Co-expression
updated 4.8 years ago by
GenoMax
154k • written 4.8 years ago by
DrEruhami
• 0
5
votes
3
replies
1.7k
views
Tumor-Normal Matched Pairwise DE using DEseq2
DESeq2
TCGAbiolinks
DE
updated 4.8 years ago by
Biostar
20 • written 4.9 years ago by
kamalikaray1792
▴ 20
2
votes
4
replies
1.0k
views
genome to exome
genome
updated 4.8 years ago by
ATpoint
90k • written 4.8 years ago by
storm1907
▴ 30
0
votes
1
reply
1.5k
views
Practical Haplotype Graph Docker Implementation Example Config File
phg
updated 4.8 years ago by
GenoMax
154k • written 4.8 years ago by
CLOE.POGODA
• 0
0
votes
6
replies
1.6k
views
How to select loops in protein structure?
protein
pdb
python
updated 4.8 years ago by
Mensur Dlakic
★ 30k • written 4.8 years ago by
qas
▴ 20
2
votes
4
replies
1.3k
views
Correct number of SNPs for gene length
SNP
4.8 years ago by
vujex
▴ 10
0
votes
2
replies
1.3k
views
errors in multiple sequencing alignment in r by use msa package!!
R
alignment
software error
updated 4.8 years ago by
Jean-Karim Heriche
27k • written 4.8 years ago by
kasemmohmmed287
• 0
2
votes
5
replies
3.0k
views
RnBeads error running rnb.run.dj()
ngs
rnbeads
methylation
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
mario.red8976
▴ 140
1
vote
1
reply
1.7k
views
cytoscape : edge weighted layout
cytoscape
updated 4.8 years ago by
scooter
▴ 650 • written 4.8 years ago by
lagartija
▴ 160
47
votes
24
replies
8.0k
views
13 follow
Forum:
What programming language do you use the most in your work? Which one do you like the best?
Programming
Python
R
Scripting
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
biotrekker
▴ 110
0
votes
0
replies
795
views
WGCNA Clinical traits file issue
wgcna
rna-seq
genome
r
R
4.8 years ago by
reara
▴ 30
1
vote
0
replies
807
views
Estimate ploidy and purity in cancer targeted sequencing
ploidy
purity
targeted sequencing
4.8 years ago by
rosefroehlich
▴ 10
4
votes
8
replies
2.4k
views
How to check wether Chip-seq worked or not
ChIP-Seq
sequencing
alignment
updated 4.8 years ago by
EagleEye
7.6k • written 4.8 years ago by
luckysardar171
▴ 20
0
votes
3
replies
1.3k
views
Merge csv files with same columns and different rows in R
R
RNA-Seq
tidyverse
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
shaden
▴ 20
3
votes
5
replies
1.4k
views
How to change sequence description automatically in an MSA
sequence
updated 4.8 years ago by
cschu181
★ 2.8k • written 4.8 years ago by
jbt38
• 0
1
vote
1
reply
1.7k
views
normalization RNASeq Data for QTL analysis
RNA-Seq
R
edgeR
DESeq
matrixQTL
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
Linda
▴ 10
2
votes
4
replies
1.4k
views
Enrichment analysis with a greater number of genes than differential expression analysis
goseq
R
RNA-Seq
4.8 years ago by
rnaka09
▴ 30
2
votes
3
replies
3.7k
views
Forum:
MOOC for AI and Machine learning for Bioinformatics
ML
AI
updated 2.7 years ago by
Ram
45k • written 5.3 years ago by
pixie@bioinfo
★ 1.5k
0
votes
1
reply
2.1k
views
Converting Bigwiggle (.bw) to bed
ChIP-Seq
4.8 years ago by
Giulia
• 0
0
votes
0
replies
834
views
Help me with ChromHMM
ChIP-Seq
4.8 years ago by
Giulia
• 0
1
vote
2
replies
1.9k
views
Annotation of pLI scores by using ANNOVAR
SNP
pLI
ANNOVAR
updated 4.8 years ago by
desouzareis.r
▴ 290 • written 4.8 years ago by
Apprentice
▴ 190
0
votes
1
reply
916
views
3 patients with 2 samples collected pre and post clinical intervention
RNA-Seq
sleuth
study design
updated 4.8 years ago by
Kevin Blighe
★ 90k • written 4.8 years ago by
lmmjrf
• 0
0
votes
1
reply
687
views
extract specific DEG from RNA-SEQ data with batch effect
RNA-Seq
4.8 years ago by
ystokar
• 0
4
votes
4
replies
3.3k
views
Append characters to end of fasta sequences in a multifasta file
fasta
sed
perl
4.8 years ago by
sid5427
▴ 20
20
votes
16
replies
4.7k
views
differential expression- coding genes
rna-seq
updated 4.8 years ago by
Kevin Blighe
★ 90k • written 4.8 years ago by
Rob
▴ 180
1
vote
0
replies
962
views
Tool:
BiOkeanos - the largest(*) biomedical database catalogue and discovery tool
database
catalogue
data
updated 2.5 years ago by
Ram
45k • written 4.8 years ago by
ellimilial
▴ 20
2
votes
1
reply
1.3k
views
3D structures of compounds
drugs
peptides
database
updated 4.8 years ago by
ellimilial
▴ 20 • written 5.3 years ago by
rob.costa1234
▴ 310
0
votes
0
replies
921
views
Issue with 2D PCA score plot in MetaboAnalystR
R
PCA
4.8 years ago by
lewhiteside
▴ 10
3
votes
4
replies
3.7k
views
Pre-processing RNAseq data before PCA or tSNE: Log-transform data?
RNA-Seq
updated 4.8 years ago by
ATpoint
90k • written 4.8 years ago by
psm
▴ 170
2
votes
4
replies
1.1k
views
where to find cancer data
SNP
cancer
next-gen
data
fastq
updated 4.8 years ago by
ATpoint
90k • written 4.8 years ago by
shubhamkumbhar420
▴ 40
0
votes
0
replies
1.1k
views
Finding Mutations in CCLE Samples
CCLE
RNA-Seq
rna-seq
gene
mutations
4.8 years ago by
mbabolda
• 0
0
votes
0
replies
2.5k
views
glimmer: Error parsing .upstream file. "Not a Fasta file?"
genome
software-error
updated 3.4 years ago by
Ram
45k • written 10.6 years ago by
SilentGene
▴ 120
0
votes
5
replies
2.7k
views
Conserved sequence for MSA
python
alignment
sequence
covid
4.8 years ago by
mhwaida258
• 0
0
votes
0
replies
873
views
Assembly based structural variants detection
Assembly
structural variants
syri
mumandco
4.8 years ago by
rthapa
▴ 90
0
votes
3
replies
1.6k
views
HTSeq Import Error Re: Working vs Build Directory
HTSeq
RNA-Seq
software error
next-gen
4.8 years ago by
James Sacco
▴ 10
0
votes
1
reply
1.4k
views
cell type specific TAD coordinates and orientations for Hi-C
sequencing
updated 4.8 years ago by
Biostar
20 • written 7.1 years ago by
alireza346
▴ 10
1
vote
1
reply
1.8k
views
extract cluters of genes from pheatmap and generate independent pheatmaps
RNA-Seq
R
heatmap
pheatmap
updated 4.8 years ago by
ATpoint
90k • written 4.8 years ago by
Maria
• 0
2
votes
5
replies
2.4k
views
Heatmap after batch correction in DESeq2
RNA-Seq
updated 4.8 years ago by
rpolicastro
13k • written 4.8 years ago by
mtsompana
▴ 10
3
votes
3
replies
1.2k
views
Searching for human genotyping data thats not public
SNP
genotyping
variants
updated 4.8 years ago by
predeus
★ 2.1k • written 4.8 years ago by
Bioinformatics-man
• 0
0
votes
0
replies
764
views
Is it possible to use vg in order to compare short sequences (100-mers)?
vg
4.8 years ago by
genomics0101
▴ 10
0
votes
0
replies
1.1k
views
Tool:
Analyze & Visualize Nephele Microbiome Results Using MicrobiomeDB
microbiome
sequence
updated 2.5 years ago by
Ram
45k • written 4.8 years ago by
karlynn.noble
▴ 60
0
votes
0
replies
607
views
Penalise trailing gaps with Bowtie2. Assume forced end-toend
Assembly
sequencing
sequence
4.8 years ago by
anonymous
• 0
2
votes
3
replies
2.9k
views
Convert processed bam file to fastq
alignment
sequence
bam
samtools
fastq
updated 4.8 years ago by
GenoMax
154k • written 4.8 years ago by
coltonrobbins73
• 0
1
vote
2
replies
2.3k
views
Using multiIntersectBed to filter original bed files
bedtools
multiIntersectBed
updated 4.8 years ago by
Alex Reynolds
36k • written 4.8 years ago by
williamtmills
▴ 20
3
votes
6
replies
4.1k
views
Batch correction in DESeq2---Normalized Counts
RNA-Seq
updated 4.8 years ago by
ATpoint
90k • written 4.8 years ago by
mtsompana
▴ 10
2
votes
1
reply
5.0k
views
Alternatives to DrugBank Database?
target
protein
drug
database
gene
updated 4.8 years ago by
ellimilial
▴ 20 • written 4.8 years ago by
cannin
▴ 350
1
vote
1
reply
1.9k
views
Filtering somatic variants (annotated VCF files)
VCF
somatic
filtering
variant
4.8 years ago by
g.zachwyc
• 0
122,217 results • Page
726 of 2445
Recent Votes
Comment: circos plot for genomic features
Answer: How to perform GO enrichment in non-model organisms?
Comment: circos plot for genomic features
Answer: How excactly is the Q30 is calculated?
A: PCA in a RNA seq analysis
what cause poly-G from NextSeq
what cause poly-G from NextSeq
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Recent Replies
Comment: Issue while running Kenddata.
by
GenoMax
154k
Look inside the `*.log` files to see if you can get additional clues (and post them here, if you can't figure out things). Check for lines …
Comment: Question about QC and scrublet
by
Arup Ghosh
3.5k
You can run Scrublet before filtering cells with high gene counts and compare the doublet score vs `n_counts_genes`.
Answer: How to perform GO enrichment in non-model organisms?
by
lieven.sterck
16k
In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed. …
Comment: circos plot for genomic features
by
Matteo Ungaro
▴ 140
@colindaven thanks a lot! `clinker` also seems to be a nice/effective tool to do so. It happens we stuble across a work where they used `Ci…
Comment: circos plot for genomic features
by
colindaven
8.1k
Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/ You can load both haplotypes, use minimap2 to create a paf …
Comment: How excactly is the Q30 is calculated?
by
colindaven
8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
Answer: How excactly is the Q30 is calculated?
by
GenoMax
154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
Comment: best practice for diploid variant calling
by
Matteo Ungaro
▴ 140
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind
by
ATpoint
90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read
by
cmdcolin
★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
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.
Comment: ID unifiying across different datasets
by
GenoMax
154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
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