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778 results • Page
1 of 16
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Votes
Replies
82
votes
46
replies
8.1k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 5 days ago by
LauferVA
4.0k • written 9 months ago by
Sasha
▴ 830
103
votes
42
replies
30k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 10 days ago by
Jeremy Leipzig
22k • written 10.4 years ago by
14134125465346445
★ 3.6k
78
votes
38
replies
32k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 18 days ago by
nickp60
▴ 60 • written 7.7 years ago by
andrew.j.skelton73
6.5k
9
votes
36
replies
12k
views
20 follow
Convert Gene IDs of Tomato Sol Database
tomato
gene
updated 27 days ago by
rafael.rubino
• 0 • written 8.7 years ago by
kevluv93
▴ 170
15
votes
34
replies
15k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq
demultiplexing
updated 12 days ago by
barslmn
★ 2.1k • written 6.6 years ago by
a.rex
▴ 350
4
votes
29
replies
10k
views
6 follow
WGCNA soft thresholding problem
WGCNA
RNA-Seq
soft thresholding
data normalization
updated 23 days ago by
foejvs546
▴ 10 • written 5.3 years ago by
catagui
▴ 40
70
votes
29
replies
14k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 5 days ago by
jkbonfield
★ 1.2k • written 5.0 years ago by
finswimmer
16k
21
votes
26
replies
9.3k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 4 days ago by
Yao
▴ 30 • written 4.3 years ago by
Juke34
8.5k
66
votes
23
replies
48k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 2 days ago by
Getnet Tesfaw
• 0 • written 6.3 years ago by
1769mkc
★ 1.1k
12
votes
19
replies
13k
views
11 follow
SnpMatrix from VCF file
VCF
Eqtl
MatrixEQTL
SnpMatrix
vcftools
updated 4 days ago by
pmiller
▴ 10 • written 7.0 years ago by
Dhana
▴ 110
75
votes
19
replies
3.2k
views
11 follow
Blog:
A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 17 days ago by
LauferVA
4.0k • written 6 months ago by
Kenny
▴ 30
12
votes
19
replies
5.1k
views
how to identify CDR region in antibody sequence
CDR
antibody
updated 18 days ago by
tiancheng
• 0 • written 21 months ago by
reany
▴ 50
0
votes
18
replies
859
views
Import list and assign distinct colors in R
R
ggplot2
5 days ago by
kmyers2
▴ 80
13
votes
17
replies
10k
views
8 follow
cutadapt for trimming reads to specific length
cutadapt
trim-galore
updated 27 days ago by
xiaoleiusc
▴ 140 • written 7.4 years ago by
Varun Gupta
★ 1.3k
4
votes
16
replies
834
views
hisat2 location does not exist
hisat2
updated 21 days ago by
Ram
43k • written 28 days ago by
Eric
• 0
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 4 hours ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
4
votes
16
replies
1.5k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools
RNAseq
samtools
BAM
updated 25 days ago by
Ram
43k • written 5 months ago by
ella
• 0
105
votes
16
replies
110k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 4 days ago by
xiaoleiusc
▴ 140 • written 11.8 years ago by
GouthamAtla
12k
25
votes
15
replies
7.5k
views
9 follow
Randomize Read Order In Multigbp Fastq File?
fastq
updated 7 days ago by
Cliff
• 0 • written 12.7 years ago by
2184687-1231-83-
★ 5.1k
7
votes
15
replies
5.5k
views
9 follow
convert VCF to gVCF
gVCF
VCF
updated 11 days ago by
jena
▴ 290 • written 4.5 years ago by
mateid
• 0
8
votes
15
replies
1.3k
views
6 follow
Novel sparse optimisation for high accuracy cancer classification on the 33-cancer TCGA gene-expression dataset
TCGA
PANCAN
cancer-classification
gene-expression
updated 13 days ago by
Jeremy Leipzig
22k • written 20 days ago by
Mark Reilly
▴ 20
3
votes
14
replies
3.9k
views
Trouble with bedtools getfasta
bedtools
getfasta
written 2.1 years ago by
gkunz
▴ 20
31
votes
14
replies
24k
views
7 follow
Difference between tSNE and PCA analysis
next-gen
rna-seq
updated 27 days ago by
Jeremy Leipzig
22k • written 6.1 years ago by
Qingyang Xiao
▴ 160
2
votes
14
replies
650
views
jellyfish installed in conda, but 'command not found' when I try to run it
jellyfish
conda
updated 26 days ago by
Joe
21k • written 27 days ago by
michael.flower.14
▴ 180
46
votes
13
replies
14k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 7 days ago by
Konstantinos
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.1k
41
votes
13
replies
25k
views
13 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq
DESeq2
geneontology
GSEA
updated 11 days ago by
CTLong
▴ 90 • written 6.4 years ago by
Sreeraj Thamban
▴ 290
0
votes
13
replies
717
views
Help with the new nomenclature of multi-nucleotide variants
bam
igv
multinucleotide
7 days ago by
amy__
▴ 160
7
votes
12
replies
637
views
ensembl - selecting SNPs of specific genes
SNP
VCF
ensembl
gene
genome
27 days ago by
Eliza
▴ 30
12
votes
12
replies
740
views
Processing fastq files for genome assembly
fastq
vcf
assembly
amino-acid
updated 9 days ago by
Brian Bushnell
20k • written 12 days ago by
Neil
▴ 20
38
votes
12
replies
18k
views
8 follow
BEDOPS gtf2bed conversion error with Ensembl GTF
gtf2bed
ensembl
bedops
gtf
updated 21 days ago by
Alex Reynolds
35k • written 7.6 years ago by
bioinformatics.cancer
▴ 260
8
votes
12
replies
13k
views
11 follow
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
updated 16 days ago by
BioinfGuru
★ 1.6k • written 3.9 years ago by
chatterjee.arumoy
▴ 50
31
votes
12
replies
773
views
7 follow
Forum:
Nextflow and self-made pipelines opinion
nextflow
pipeline
data-analysis
19 days ago by
karlaarz
▴ 90
3
votes
12
replies
595
views
bbmap read length from fastq
fastq
bbmap
updated 4 days ago by
GenoMax
140k • written 10 days ago by
marco.barr
▴ 30
3
votes
12
replies
4.2k
views
samtools mpileup keeps making an empty file
samtools
pileup
updated 18 days ago by
gabt
▴ 120 • written 5.2 years ago by
James Reeve
▴ 130
8
votes
12
replies
970
views
7 follow
How to speed-up to contruct phylogenetic tree
MEGA
tree
phylogenetic
updated 6 days ago by
Joe
21k • written 3 months ago by
Nelo
▴ 20
0
votes
12
replies
523
views
BWA MEM different synthax on linux (bash) and macOS (zsh)
MEM
BWA
11 days ago by
gernophil
▴ 80
4
votes
11
replies
3.5k
views
9 follow
ADMIXTURE Segmentatio fault
admixture
plink
vcf
updated 28 days ago by
MsMalteze2011
• 0 • written 2.8 years ago by
pmc.sa
▴ 40
2
votes
11
replies
634
views
Reference Guided genome assembly
tabix
updated 24 days ago by
Michael
54k • written 25 days ago by
sainavyav22
• 0
0
votes
11
replies
620
views
Filtering VCF based on codon-transcript
vcf
bcftools
updated 2 days ago by
barslmn
★ 2.1k • written 13 days ago by
avelarbio46
▴ 30
2
votes
10
replies
518
views
Can't properly use GATK Mutect2 to call somatic variants from my tumor/normal samples pair (BAM to VCF)
vaf
gatk
vcf
genomics
mutect2
updated 5 days ago by
GenoMax
140k • written 6 days ago by
Samuel
▴ 20
6
votes
10
replies
2.6k
views
How can Investigate if a Viral genome is circular or linear? And if it is single or double stranded?
Assembly
genome
updated 17 days ago by
Israel
• 0 • written 5.3 years ago by
GiV17
▴ 50
18
votes
10
replies
5.1k
views
Should I normalize read counts if I want to run plotPCA?
RNA-Seq
updated 10 days ago by
ella
• 0 • written 3.9 years ago by
c_u
▴ 520
2
votes
10
replies
664
views
RNA seq aligner?
Alignment
updated 4 days ago by
Dave Carlson
★ 1.6k • written 13 days ago by
tesfaye
• 0
0
votes
10
replies
584
views
Denovo transcriptome assembly
Denovo
assembly
transcriptome
25 days ago by
prs
• 0
3
votes
10
replies
528
views
Errors running PHG MakeInitialPHGDBPipelinePlugin (**UNASSIGNED**)
pangenome
plants
PHG
updated 4 days ago by
lcj34
▴ 390 • written 7 days ago by
b.contreras.moreira
▴ 10
10
votes
10
replies
679
views
Message seen when performing alignment
bwa
alignment
updated 25 days ago by
GenoMax
140k • written 27 days ago by
K
• 0
0
votes
10
replies
735
views
Problem running scPred
scPred
scPredict
updated 5 days ago by
Ram
43k • written 10 weeks ago by
Nitin
• 0
4
votes
10
replies
581
views
PDB residue serial inconsistency and PDB id&UniProt ID mismatch
pdb
UniProtID
pdbID
updated 18 days ago by
Wayne
★ 1.9k • written 19 days ago by
Nafi
• 0
3
votes
10
replies
631
views
t-test in two groups, multiple rows
R
t-test
12 hours ago by
sooni
▴ 20
16
votes
10
replies
10k
views
8 follow
GRCh37.p13 download at NCBI FTP?
ncbi
reference
grch37
updated 9 days ago by
Sruthi
• 0 • written 5.5 years ago by
Marvin
▴ 220
778 results • Page
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Recent Votes
UniprotKB BLAST pipeline troubles
UniprotKB BLAST pipeline troubles
Comment: UniprotKB BLAST pipeline troubles
Answer: UniprotKB BLAST pipeline troubles
Cross-referencing Id from Swiss-Prot/UniProtKB human reference proteome to Ensembl Genes
Answer: Cross-referencing Id from Swiss-Prot/UniProtKB human reference proteome to Ensem
why there is an asterisk symbol at the end of each proteins sequences offasta files in the Braker3 output FASTA file?
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Comment: Single cluster spanning in different locations in UMAP in scRNAseq data
by
ATpoint
81k
It means that there is a disagreement between UMAP and clustering algorithm, but since UMAP is mostly just visualization you could ignore i…
Comment: Ribo and RNA seq analysis
by
Jack Tierney
▴ 350
Hi Manu Ayllon, It is difficult to advise as I am unclear on the goal of your project. I will tell you what I understand and you can co…
Answer: Ribo and RNA seq analysis
by
Manu Ayllon
• 0
I got it making use of blastn, creating first a database with the RNA sequences and doing blast with the Ribo-seq sequences as query. The p…
Comment: Deeptools scale issue for plotHeatmap
by
Learner
• 0
Hi Devon, Thanks a lot for the reply. DNA methylation file has 19466838 lines while domains has 92409 lines.
Answer: why there is an asterisk symbol at the end of each proteins sequences offasta fi
by
Juke34
8.5k
It corresponds to stop codon but in theory GTF format does not have stop codon in CDS. Keep in mind that it exists stop codon reading th…
Comment: scRNAseq normalization
by
ATpoint
81k
That is an entirely different analysis and depends on the testing Framework. If you use the commonly-used Wilcox test or something like lim…
Comment: Haddock 2.4
by
Preeti
• 0
i have three different runs with haddock score of -75, -68, -61 . Which one is better among these( molecule 1 is same in all three ,only mo…
Comment: NGS/GATK pipeline returns too many variants
by
dhruti
• 0
@dodausp Did you ever find a reason for this? I am having the same problem
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Corentin
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Sex chromosomes are always a bit tricky to handle in associations studies. How many male cases and male controls you have for this phenoty…
Comment: Beagle Phasing and Imputation
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Duarte Molha
▴ 240
Hi @lchart Thank you for your answer. I coded my male sample as biallelelic homozygous as i was aware of limitations for allosomes.…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Dora
▴ 10
And I also change the chrom name in the .sizes file. That works perfect. Thank you very much!
Comment: scRNAseq normalization
by
sarahmanderni
▴ 100
Thanks for the response! I also was wondering to ask if you have found the log-norm also working fine in terms of downstream analysis like …
Answer: Subsetting Seurat object based on list of cell barcodes
by
fracarb8
★ 1.5k
`subset(seurat.obj_combined, cells = all_good_cells_rhemac10$V1)` You need to pass `cells` not `subset`. From the documentation: sub…
Answer: TCGA UUIDS to TCGA barcode (SampleID) in R
by
aUser
▴ 30
Great solutions on this page, the old web page has been replace with new one, so you need to use the new link, and it will work: old lin…
Comment: Issues With Cram -> Fastq from GTEx v8 WGS
by
Pierre Lindenbaum
160k
unless your cram in sorted on query rather than on coordinate, your cram must be first sort processed with collate: https://twitter.com/lh…
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