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122,200 results • Page 626 of 2444
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2
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730
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panelcn.mops package to build up control.bam file
panelcn.mops samtools
4.4 years ago by jimmy0958073736 ▴ 40
1
vote
3
replies
1.3k
views
Blast results processing lines bigger than 60
blast unix commands awk result
4.4 years ago by hdtms ▴ 20
0
votes
14
replies
2.8k
views
error relate to R
TWAS SNP R
updated 4.4 years ago by ★ 90k • written 4.4 years ago by ▴ 150
1
vote
0
replies
1.2k
views
DepthPerSampleHC and StrandBiasBySample HaplotypeCaller Warnings in GATK
Haplotypecaller
4.4 years ago by Jianing ▴ 10
2
votes
0
replies
684
views
scRNA-seq datasets for different cell lines
scRNAseq
4.4 years ago by Alexander ▴ 220
2
votes
9
replies
3.3k
views
Getting command line blastn results for the complementary strand
blast command-line blastn
updated 4.4 years ago by 16k • written 4.4 years ago by ▴ 70
2
votes
2
replies
1.3k
views
Differentially gene expression multispecies
Gene Expression Multiespecies RNAseq
4.3 years ago by tiagobellintani ▴ 40
3
votes
2
replies
1.4k
views
Differentially gene expression analysis using limma
Limma packages
updated 4.4 years ago by 3.3k • written 4.4 years ago by ▴ 20
2
votes
5
replies
2.8k
views
Weird characters in yeast reference gff3
SGD gff3 yeast gff
4.4 years ago by liorglic ★ 1.5k
7
votes
3
replies
2.0k
views
How to normalize and transform RNA-seq data of different samples for PCA?
TMM PCA RNA-seq edgeR
updated 4.4 years ago by ★ 90k • written 4.4 years ago by ★ 1.1k
0
votes
2
replies
2.3k
views
Manhattan plot p-value
manhattan plot snp
4.4 years ago by shamsurrahaman132 ▴ 10
0
votes
0
replies
676
views
IGV add contig/chr to genome file within session
genome IGV bam alignment
4.4 years ago by noodle ▴ 650
0
votes
1
reply
1.2k
views
Which error bar to use to show gene expression from single-cell RNAseq data
expression rnaseq statistics gene single-cell
4.4 years ago by gundalav ▴ 380
0
votes
0
replies
1.8k
views
Generating comprehensive data for Promethease and Codegen.eu from WGS
WGS gVCF Promethease raw calling variant
4.4 years ago by Tim • 0
0
votes
0
replies
710
views
rsem-calculate-expression error
RNA-Seq rsem rsem-calculate-expression
4.4 years ago by Bhoomika • 0
3
votes
4
replies
1.6k
views
How to calculate the distribution of histone modifications on transcription factors
modifications histone
4.4 years ago by koyee_d ▴ 20
2
votes
2
replies
2.7k
views
How to convert genotypes "1, 2" to "0,1, 2"?
snp plink
updated 2.2 years ago by ▴ 10 • written 4.4 years ago by ▴ 50
0
votes
2
replies
1.0k
views
Extracting coding region for multiple sequences.
Coding Region
4.4 years ago by QAZ ▴ 20
2
votes
8
replies
5.4k
views
Trying to run FIMO from Meme suite using command line
meme motif
updated 4.4 years ago by 11k • written 4.4 years ago by • 0
3
votes
3
replies
1.2k
views
How to identify and characterize novel genes?
Novel
updated 4.4 years ago by ▴ 590 • written 4.4 years ago by • 0
0
votes
0
replies
699
views
How was hierarchical clustering established for mRNA expression data?
clustering mRNA expression
4.4 years ago by ceruleanivy ▴ 50
0
votes
1
reply
1.2k
views
Help with processing GSE63060: Illumina data that does not have lumi requirements
lumi illumina Bioconductor R
updated 4.4 years ago by ★ 90k • written 4.4 years ago by • 0
1
vote
1
reply
1.2k
views
Minimum coverage for structural variant calling
variant structural coverage
updated 4.4 years ago by ★ 2.2k • written 4.4 years ago by ▴ 370
11
votes
10
replies
12k
views
7 follow
How To Calculate Genetic Heterogeneity From Genotype Data - How Useful Is This Measure?
genetics snp genotyping
updated 3.7 years ago by 45k • written 14.8 years ago by 16k
1
vote
3
replies
4.2k
views
Adding a chain ID (A or B etc) to my pdb file
pdb
updated 4.4 years ago by • 0 • written 4.8 years ago by • 0
0
votes
3
replies
4.0k
views
Problems running gatk - gatk: command not found
vcf bam gatk
updated 4.4 years ago by ★ 1.2k • written 4.4 years ago by ▴ 210
1
vote
0
replies
844
views
Job: Computational research positions, incl. postdoctoral scholars (recommender systems in genomics)
recommender Seattle visualization genomics
4.4 years ago by meuleman ▴ 10
0
votes
1
reply
1.3k
views
Exporting Genes/Molecules of interest from IPA Canonical Pathway
core export data analysis ipa
updated 4.4 years ago by • 0 • written 4.4 years ago by • 0
1
vote
3
replies
1.6k
views
TEMP ,Type checker found wrong number of fields while tokenizing data line.
bedtools TEMP transposabale elements
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
0
votes
3
replies
1.1k
views
Tripal Fancy Fields
tripal
updated 4.4 years ago by ★ 90k • written 4.4 years ago by ▴ 120
2
votes
2
replies
1.3k
views
How much would it cost to do a de novo assembly (plus annotation) of a jellifish genome?
novo genome de assembly budgeting
4.3 years ago by ilante ▴ 30
1
vote
3
replies
1.4k
views
how to do make differential expression of lncRNA from RNA-seq data
lncRNA mRNA RNA-seq
updated 4.4 years ago by ★ 2.6k • written 4.4 years ago by ▴ 30
1
vote
3
replies
1.7k
views
Filtering nuclear RNA expression instead of MT expression in Scanpy
filtering nRNA scanpy scRNAseq mtRNA
updated 2.9 years ago by • 0 • written 4.4 years ago by • 0
2
votes
3
replies
1.5k
views
How can download and read BAM and FASTQ format
fastq miseq BAM
updated 4.4 years ago by 15k • written 4.4 years ago by • 0
1
vote
3
replies
2.3k
views
log2 normalization produces NaNs
r
updated 3.0 years ago by 45k • written 4.4 years ago by ▴ 70
0
votes
1
reply
1.4k
views
RnBeads Greedycut command ???
greedycut rnbeads array methylation
updated 4.4 years ago by • 0 • written 5.2 years ago by ▴ 520
0
votes
3
replies
1.2k
views
Phylogeny Analysis tools
Phylogeny
updated 4.4 years ago by ★ 2.9k • written 4.4 years ago by ▴ 20
0
votes
3
replies
1.3k
views
how can I get alignment quality from bam index file?
NGS samtools galaxy
updated 2.4 years ago by 45k • written 4.4 years ago by ▴ 30
2
votes
5
replies
2.0k
views
Issue installing Plink
Plink
4.4 years ago by AndrMod • 0
3
votes
2
replies
1.1k
views
Suggestions for an undergraduate research project on glioblastoma
glioblastoma Python Cancer R
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 100
7
votes
7
replies
10k
views
Mummer To Viewable Alignment Format (Fasta Or Aln...)
genomics alignment
updated 4.4 years ago by • 0 • written 14.2 years ago by ★ 2.5k
0
votes
0
replies
1.1k
views
how to get effect sizes (R2) in result of GEMMA?
GEMMA SNP
updated 2.7 years ago by 45k • written 4.4 years ago by ▴ 170
0
votes
0
replies
646
views
miRNA to families
python families RNAseq miRNA R
4.4 years ago by ehruan ▴ 10
2
votes
7
replies
2.6k
views
Good QC Package (RSeQC or alternative) for Salmon mapping/quantification results?
RSeQC Salmon RNA-Seq mapping
updated 7 months ago by • 0 • written 4.4 years ago by ▴ 80
3
votes
0
replies
3.6k
views
Why does the Seurat FindMarkers function report different log fold change values than the FoldChange function?
single scRNA-seq cell RNA-Seq Seurat
4.4 years ago by imdoingascience ▴ 40
0
votes
1
reply
2.0k
views
High levels of duplicated reads Illumina from PCR-free libraries
fastqc PCR duplicate reads Illumina
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 40
12
votes
5
replies
1.8k
views
how to sort the rows of a file as a matrix?
linux
updated 2.1 years ago by 45k • written 4.4 years ago by • 0
2
votes
2
replies
2.1k
views
WGCNA - GTEx RNASeq - Help choosing a soft power
WGCNA RNA-Seq GTEx
4.4 years ago by Branden • 0
0
votes
0
replies
502
views
How to deal with fractional number for enrichment analysis
protein analysis enrichment
4.4 years ago by Cancan • 0
0
votes
2
replies
2.0k
views
Normalization/Scaling with sctransform in RStudio of scRNASeq data
vst normalization sctransform scRNASeq scaling
4.4 years ago by ConfusedSheep ▴ 10
122,200 results • Page 626 of 2444
Recent Votes
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Can i use orthofinder for small protein datasets and not full proteome?
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Answer: Midpoint rooting IQTREE newick file moves node support around
Answer: Subsetting before QC in Spatial Transcriptomics
Answer: Feature Counts vs Salmon quantification
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Teacher to dthorbur ★ 3.2k
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Recent Replies
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by michael.ante ★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome? by dthorbur ★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
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