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0
votes
1
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16
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Installing perl modules on a conda environment produce changes out of the environment?
conda perl
updated just now by 6.9k • written 2 hours ago by ▴ 10
0
votes
0
replies
27
views
Codon alignment with degenerate nucleotides?
paml codeml codon alignment
4 hours ago by DNAlias ▴ 10
583
votes
155
replies
64k
views
89 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook tutorial training News
updated 8 days ago by 10 • written 4.4 years ago by 87k
1
vote
1
reply
48
views
Make New Orig.ident in seurat object or
R RNA-SEQ Seurat
updated 8 hours ago by ▴ 140 • written 9 hours ago by • 0
0
votes
1
reply
74
views
RNAseq
gffcompare error stringtie rnaseq
updated 7 hours ago by 72k • written 9 hours ago by • 0
1
vote
2
replies
77
views
Duplicated Gene Symbol names after geneID conversion
geneID
updated 9 hours ago by 99k • written 10 hours ago by ▴ 70
1
vote
1
reply
65
views
How to merge two GTFs which share some common features
stringtie GTF annotation
10 hours ago by emalekos • 0
0
votes
0
replies
38
views
my gffcompare out put gtf file is like that. on complete row is followed by some uncomplete row wich have not class codes.
gffcompare rna lncrna gtf
updated 13 hours ago by 99k • written 16 hours ago by • 0
0
votes
0
replies
42
views
Skewed Betweenness Centrality values resulting in almost unusable PPI networks for my university project - what can I do?
Bioinformatics Cytoscape
17 hours ago by gemmalouisebaldock ▴ 20
1
vote
1
reply
80
views
Performance metrics of aligners and variant callers
benchmarking WGS
updated 16 hours ago by 20k • written 21 hours ago by ▴ 10
2
votes
2
replies
135
views
News: Bioinformatics Solutions on AWS
AWS Bioinformatics Cloud
16 hours ago by Jillian ▴ 20
6
votes
11
replies
359
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq DESeq2
47 minutes ago by sumitguptabt ▴ 10
0
votes
1
reply
62
views
making a PCA from MASH distance result
MASH R PCA
updated 22 hours ago by 9.7k • written 23 hours ago by ▴ 10
0
votes
0
replies
45
views
Query on miRDeep2
mirDeep2 mapper
updated 21 hours ago by 5.6k • written 1 day ago by • 0
3
votes
2
replies
156
views
Negative values in Cox regression analysis
survival CoxPH coxregression
1 day ago by Mran ▴ 20
2
votes
1
reply
124
views
Bam file metrics
ngs bam gatk
updated 1 day ago by 99k • written 1 day ago by • 0
0
votes
2
replies
171
views
bedtool closest
bedtool
updated 9 hours ago by 32k • written 1 day ago by • 0
2
votes
3
replies
217
views
Visualize DNA sequence as a dot plot?
plot visualization DNA dot
updated 1 day ago by 32k • written 5 days ago by • 0
0
votes
0
replies
68
views
How should we replace NAs from a genelight object?
R glpca adegenet GBS SNP
1 day ago by jaafari.omid ▴ 50
1
vote
2
replies
109
views
To create amino acid substitution in protein structure
protein bioinformatics software
21 hours ago by shwetamgr1 • 0
0
votes
1
reply
73
views
Protein-Protein interaction for Upregulated genes
STRING DEGs PPI
updated 1 day ago by ★ 10k • written 1 day ago by • 0
0
votes
2
replies
89
views
Geno Ontology Analysis
GO hypergtest
updated 1 day ago by 32k • written 1 day ago by • 0
1
vote
3
replies
207
views
How to retrieve protein sequence from gene ID and output a fasta file
ncbi gene protein biopython entrez
updated 1 day ago by 99k • written 2 days ago by • 0
0
votes
0
replies
43
views
drug resistance informations for variations
cosmic somatic drug variants germline
1 day ago by enes • 0
0
votes
1
reply
64
views
DiffBind consensus peak extraction
DiffBind ChIP-seq
updated 1 day ago by ★ 1.0k • written 1 day ago by • 0
1
vote
2
replies
80
views
hisat2 output from paired en reads.
hisat2 rna-seq
updated 1 day ago by ★ 1.7k • written 1 day ago by ▴ 30
1
vote
2
replies
92
views
GATK variant annotation
vcf gatk
updated 1 day ago by 32k • written 1 day ago by • 0
0
votes
0
replies
49
views
Assembly pipeline for SMRT (PacBio) sequenced bacterial genome data?
sequence genome perl python pipeline
1 day ago by Kumar ▴ 50
0
votes
0
replies
33
views
MACS2 Summit TSSPlot dividing BDG into bins
TSS Callpeaks MACS2
1 day ago by Seigfried ▴ 70
0
votes
0
replies
1.8k
views
Include - in part of the motif for analysis? And "It looks like we don't support this file format" when opening weblogo motif
motif aminoacids sequence biopython weblogo
1 day ago by minifoog • 0
0
votes
0
replies
87
views
LD score regression of data including SNPs with extremely low P-value
heritability SNP LDSC
1 day ago by Apprentice ▴ 50
0
votes
1
reply
109
views
gRNA concatamer - will it work ?
gRNA CRISPR PAM
updated 1 day ago by 48k • written 2 days ago by • 0
3
votes
1
reply
77
views
Understanding the ColData Matrix
RNA-SEQ R Micheal_Love DESEQ2
updated 2 days ago by 9.3k • written 2 days ago by ▴ 30
0
votes
0
replies
121
views
Job: Bioinformatician/Programmer at the University of Pennsylvania
pipelines programmer bioinformatician python r
2 days ago by adamnaj • 0
0
votes
0
replies
71
views
Job: Bioinformatician at Turbine / Hungary
proteomics cancerreserach singlecell python r
2 days ago by timea.volenter • 0
0
votes
0
replies
45
views
panel of normals for mutect2
mutect2 gatk NGS PoN somatic
2 days ago by lait ▴ 160
0
votes
2
replies
102
views
format conversion using OpenBabel
software
1 day ago by roybatty269 • 0
0
votes
0
replies
55
views
How to compare enrichment scores?
enrichment scores
2 days ago by fpizzagalli • 0
0
votes
0
replies
47
views
Should I take FDR < 0.2 for differentially abundant bacteria found in meta-analysis random effect ?
FDR Microbiome
2 days ago by deep771992chanda ▴ 30
0
votes
1
reply
80
views
Program for predicting RNA sequences that may bind to a protein Domain
protein Binding domain RNA
updated 2 days ago by ★ 10k • written 2 days ago by ▴ 10
2
votes
5
replies
273
views
Understanding TCGA's ASCAT copy number data
tcga ascat copy number
updated 2 days ago by ▴ 280 • written 6 weeks ago by ▴ 70
0
votes
1
reply
122
views
GDC Data Query
RNA-Seq
updated 2 days ago by ▴ 280 • written 4 weeks ago by • 0
1
vote
3
replies
105
views
Redundancy reduction of de novo transcriptome assemblies with Compacta?
de-novo transcriptome redundancy-reduction
1 day ago by Dunois ▴ 630
0
votes
5
replies
156
views
Cellranger count.srun issues
cellranger srun
updated 2 days ago by 99k • written 2 days ago by • 0
1
vote
2
replies
122
views
Up-to-date GWAS Power Calculator and GWAS power comparison
GWAS power
7 hours ago by moxu ▴ 480
1
vote
1
reply
2.3k
views
How to design WGCNA: one analysis over all sample or seperate analysis (using consensus module analysis)?
WGCNA RNA-seq
updated 2 days ago by 72k • written 4 days ago by ▴ 10
3
votes
2
replies
164
views
Contradiction in Harzard ratio and Log fold change
Foldchange Cancer HR HarzardRatio LogFC
1 day ago by Mran ▴ 20
0
votes
0
replies
49
views
Refs/tools for protein interactomes
Protein PSI-MI Interactome Orthologs PPI
2 days ago by ian.will • 0
0
votes
4
replies
163
views
How to plot a image like this.
plot Bioinformatics Cancer R Genome
2 days ago by lincaijin1994 • 0
1
vote
2
replies
132
views
HaplotypeCaller VCF depth is greater than the number of reads in bam
HaplotypeCaller vcf gatk
2 days ago by wang.yiguan • 0
90,538 results • Page 1 of 1811
Recent Votes
Comment: RNAseq data analysis of pooled data
Answer: RNAseq data analysis of pooled data
Normalisation of read mapping counts to account for contig length
Answer: Limiting variant calls to amplicon target regions?
Converting TCGA expression data from FPKM to TPM
C: Raw counts to TPM in R
Answer: Duplicated Gene Symbol names after geneID conversion
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Recent Replies
Comment: single tumor vs multiple normal sample differential gene expression (RNA-Seq ) a by sumitguptabt ▴ 10
Dear, please help me, I am new in this field. Please tell me if it is the right way or needs some correction.
Comment: RNAseq by Kevin Blighe 72k
Hi, can you please choose a more informative question title? Also, can you take a look at how I use `gffread`, here: https://www.biostars.…
Comment: Up-to-date GWAS Power Calculator and GWAS power comparison by moxu ▴ 480
Hi Kevin, Thanks for the reply. I had checked out CaTS before posting above. However, I am not sure if CaTS does what I want to do. Suppo…
Comment: Arlequin problem (different loci number among different genotypes) by wangh920 • 0
For sure, The reason why this happen is because SNP calling generate a couple of biallelic SNP, such as GC, GT or GCT, GCG. These allelic…
Answer: Make New Orig.ident in seurat object or by fracarb8 ▴ 140
You can use `strsplit` to extract the first entry before the `_` metadata <- seurat_object@meta.data metadata$orig.ident <- …
Comment: How to solve the problem when I get error message "column 1 is not a genotype ob by Bornali • 0
Hi Devon Ryan. I am trying to add genotype object to my SNP data set. I am unable to use the codes described in the subsequent comment as m…
Comment: Duplicated Gene Symbol names after geneID conversion by asumani ▴ 70
opss, didn't notice that thread. many thanks!
Answer: Duplicated Gene Symbol names after geneID conversion by GenoMax 99k
See: https://www.biostars.org/p/352492/#352535
Comment: Can't count features with featurecount by avelarbio46 ▴ 10
After using these options, I got decreased aligment in general than with "-F GTF -s 0 -p -T 8 -a ". I have not tried with -M and -O on 1 or…
Comment: How to merge two GTFs which share some common features by GenoMax 99k
See the answers and discussion in: https://www.biostars.org/p/9465577/
Comment: single tumor vs multiple normal sample differential gene expression (RNA-Seq ) a by sumitguptabt ▴ 10
Dear @atpoint Thank you so much for your help, I can not describe my happiness. I run your script and got the output as you see in the att…
Comment: How to run SPAdes assembler with bam files? by GenoMax 99k
Sorted files compress better so the size being smaller is not a particular surprise. Have you checked to see that you are getting reads at …
Comment: How to run SPAdes assembler with bam files? by marongiu.luigi ▴ 560
Thank you. Actually I am getting an unmapped.bam file of 132 Mb, a sorted version of 34 Mb (shouldn't they be the same weight) and fastq of…
Comment: Bioinformatics Solutions on AWS by Jillian ▴ 20
I had that pointed out to me, but thanks for the heads up! I know it's a problem. I wrote the book using Sphinx, and I have to figure out h…
Comment: Performance metrics of aligners and variant callers by Devon Ryan 98k
Have you searched pubmed? By now there must be hundreds of papers that do this. Just read a few if you're uncertain which tools might work …
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