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0 votes
9 replies
4.2K views
keep getting error with psiblast
psiblast python blast
updated by fznajar • fznajar • written by Mo Mo
0 votes
2 replies
1.2K views
Normalization of Bigwig file
atac bigwig
updated by Ram Ram • written by daffodil • daffodil
0 votes
2 replies
1.1K views
genomecov -d -pc -ibam showing no coverage for every position
transcriptomics genomecov bedtools rna-seq
updated by ATpoint ATpoint • written by Gabrielle • Gabrielle
0 votes
1 reply
1.0K views
LOFTEE flag on GnomAD - END_TRUNC
loftee gnomad
updated by Pierre Lindenbaum Pierre Lindenbaum • written by hello_bioinf • hello_bioinf
0 votes
2 replies
880 views
Difference in count values depends on tool and reference genome version
rna-seq
updated by Ram Ram • written by shome • shome
0 votes
2 replies
1.3K views
Bayesian Differential Expression
deseq2 edger limma bayesian
written by thyleal thyleal
0 votes
2 replies
1.8K views
Fast tool for FASTQ Q30 calculation
q30 fastq q20
updated by Ram Ram • written by emma.a • emma.a
0 votes
0 replies
653 views
ChromVAR filterPeaks error
atac-seq chromvar filferpeaks
written by maplewj • maplewj
1 vote
0 replies
758 views
Deconvolution: bulk and cell signature data from different platforms or technologies
cibersort rnaseq microarray deconvolution signature
written by zhang.jianhai • zhang.jianhai
0 votes
2 replies
957 views
Processing FASTQ Files
viewing fastq metrics
written by Carla • Carla
1 vote
1 reply
1.0K views
Cytoscape to visualize metanodes
graph examine cytoscape
updated by xanderpico xanderpico • written by Giovanni • Giovanni
1 vote
8 replies
2.3K views
Can edgeR be used to find (over/under)represented sequences in fastq files?
fastq edger rnaseq
written by AquaDeath • AquaDeath
0 votes
3 replies
3.2K views
samtools index error - "Unsorted positions on sequence" even though file is sorted
samtools alignment bam
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Geoffrey • Geoffrey
0 votes
5 replies
1.8K views
Blastn frozen
blastn ncbi blast remote-blast
written by Begonia_pavonina • Begonia_pavonina
0 votes
2 replies
1.4K views
3 questions about module membership vs gene significance
wgcna
updated by Mensur Dlakic Mensur Dlakic • written by demoraesdiogo2017 • demoraesdiogo2017
0 votes
9 replies
3.0K views
How to accelerate BLASTING
ncbi blast sequence
written by anikcropscience • anikcropscience
0 votes
5 replies
2.0K views
AlphaFold2 Colab
alphafold
updated by Ram Ram • written by Preeti • Preeti
0 votes
3 replies
3.2K views
Trying to work with the NCBI's Entrez api using python.
biopython python ncbi
updated by ninastanisic4 • ninastanisic4 • written by gdizzle12 • gdizzle12
0 votes
2 replies
1.3K views
Deep Sequencing vs Shallow Sequencing but repeated several times
transcriptomics star rnaseq
updated by dthorbur dthorbur • written by andrebolerbarros • andrebolerbarros
0 votes
1 reply
929 views
Heteroscedasticity in RNA-seq data
rna-seq statistics
updated by i.sudbery i.sudbery • written by ToTheMoon • ToTheMoon
0 votes
1 reply
1.5K views
phyloseq_filter_prevalence, non zero dimension
phyloseq
updated by Yunliang • Yunliang • written by junghwachoi96 • junghwachoi96
0 votes
5 replies
1.3K views
Count table statistical analysis
count-table statistical-analysis
updated by Ram Ram • written by ToTheMoon • ToTheMoon
0 votes
1 reply
803 views
Cytoscape for set-oriented Analysis of different species
graph examine cytoscape
updated by xanderpico xanderpico • written by Giovanni • Giovanni
0 votes
3 replies
1.5K views
Problem with SUPPA2 Psi calculation
alternative-splicing suppa2
updated by Ram Ram • written by achanda • achanda
0 votes
0 replies
627 views
sequencing results of CRISPR base edit
crispr chromatogram
updated by Ram Ram • written by hmiller • hmiller
0 votes
1 reply
1.3K views
question on how differential expression is affected if there is differential abundance between celltypes
differential-abundance scrna-seq differential-expression
updated by i.sudbery i.sudbery • written by lordoftheflower • lordoftheflower
0 votes
1 reply
1.0K views
Pseudo bulking of scATAC-seq
scatac-seq signac
updated by jared.andrews07 jared.andrews07 • written by Manhezz • Manhezz
0 votes
1 reply
882 views
what is the best database for fusion genes ?
rna-seq fusion-genes
updated by Yogi • Yogi • written by Lila M Lila M
0 votes
1 reply
783 views
how to extract alignment concordantly exact 1 time from bowtie2 output
bowtie2
updated by GenoMax GenoMax • written by Wasim • Wasim
0 votes
0 replies
707 views
bcftools Haploid variant calling
bcftools
written by Wasim • Wasim
0 votes
0 replies
1.1K views
TSS Enrichment error in Signac
signac scrna-atac ensdb
written by kousi31 • kousi31
0 votes
14 replies
2.6K views
frma normalization
affybatch frma mcp-counter
written by michelafrancesconi9 • michelafrancesconi9
0 votes
2 replies
970 views
Snakemake Wildcard Issue: Trouble Passing Config Field to Rule Input
python snakemake
written by blackadder • blackadder
0 votes
3 replies
1.3K views
Can you suggest tools or script to get canonical sequences from a cds fasta file?
genome cds fasta
updated by Ram Ram • written by Yuto • Yuto
0 votes
2 replies
1.3K views
Linux dependencies in Docker file
linux docker
updated by ATpoint ATpoint • written by mrashad mrashad
0 votes
3 replies
1.2K views
Getting less DE genes when incorporating all samples
rna-seq differential-expression deseq2
updated by jv jv • written by shome • shome
0 votes
0 replies
551 views
miseq double band
adapter index double-band pcr miseq
written by junghwachoi96 • junghwachoi96
0 votes
12 replies
2.7K views
ensembl - selecting SNPs of specific genes
snp vcf ensembl gene genome
written by Eliza • Eliza
1 vote
0 replies
794 views
Alternatives to mirBase for mirDeep2 Input
mirbase rnacentral ferret rnaseq mirdeep2
written by Jack • Jack
1 vote
7 replies
4.6K views
Blast NCBI online using R
r ncbi blast rstudio
written by Begonia_pavonina • Begonia_pavonina
4 votes
10 replies
13K views
Free Virtual Ligand Screening Software
drug software
updated by Jasper • Jasper • written by Wayne Wayne
0 votes
1 reply
746 views
1000 genome project specific genes selection
gwas 1000genomes
updated by Ram Ram • written by Eliza • Eliza
0 votes
1 reply
2.2K views
How to solve unloadNamespace(package) : namespace in R
r
updated by Ram Ram • written by kousi31 • kousi31
0 votes
6 replies
2.0K views
vcftools warnings worrisome?
vcftools
updated by Ram Ram • written by 8armed • 8armed
0 votes
0 replies
587 views
Tool: Annotating the epitope-specificity of TCRs with bioinformatics
annotation tcr epitope-specificity
written by tim • tim
0 votes
0 replies
1.1K views
Deviance for feature selection in Seurat
feature-selection seurat
written by Immreg • Immreg
0 votes
0 replies
522 views
Discovery of reads originating from the chloroplast with multiple congeners' reference
non-model-species mapping congener chloroplast
updated by Ram Ram • written by Plant_man_217 • Plant_man_217
0 votes
2 replies
1.1K views
attempting to download eQTL data from eQTL catalog, but code not retrieving file
gwas eqtl genomics
written by Orlando • Orlando
0 votes
4 replies
1.1K views
Differential methylation in gene
differential-methylation
written by Mamatha Y S • Mamatha Y S
0 votes
7 replies
1.7K views
Extract SNPs present in mutants
snp vcftools vcf bcftools
updated by Pierre Lindenbaum Pierre Lindenbaum • written by pablo pablo
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