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1.6k
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How to interpret logistic interaction results from plink2 output?
SNP plink GWAS interaction logistic
updated 4.8 years ago by ★ 90k • written 5.7 years ago by • 0
0
votes
2
replies
1.6k
views
Arrow crashes during second iteration
genome polish arrow gcpp
4.8 years ago by elcortegano ▴ 210
0
votes
2
replies
1.5k
views
How to analyse lncRNA
RNA-Seq
updated 4.8 years ago by ▴ 520 • written 4.8 years ago by • 0
0
votes
2
replies
1.6k
views
Merging overlapping mates in a BAM / SAM file into one read
RNA-Seq
4.8 years ago by lechu ▴ 20
0
votes
1
reply
1.4k
views
List of good CNV detection methods?
CNV algorithm
4.8 years ago by 860101959 ▴ 10
1
vote
5
replies
2.5k
views
Size difference using gunzip-cat-gzip and zcat
RNA-Seq sequencing
updated 4.8 years ago by 45k • written 4.8 years ago by ▴ 140
6
votes
7
replies
2.3k
views
How to record Seurat DE analysis efficiently?
R RNA-Seq rna-seq
4.8 years ago by Pratik ★ 1.1k
8
votes
4
replies
18k
views
Seurat "FindMarkers" and "FindallMarkers" v.s. Scanpy "rank_genes_groups"
scRNA Seurat R single-cell Scanpy
updated 4.8 years ago by ▴ 50 • written 5.3 years ago by ▴ 20
0
votes
0
replies
569
views
is it ok for two subspecies sharing one HI-C data ?
assembly
updated 4.8 years ago by 20 • written 4.9 years ago by • 0
4
votes
8
replies
6.6k
views
How can I convert from bed to bed12 format?
BED bed12
updated 4.8 years ago by ▴ 130 • written 7.6 years ago by ▴ 610
0
votes
1
reply
1.4k
views
Beagle conform-gt error
Beagle conformgt imputation java tomped
4.8 years ago by kstafford32 • 0
5
votes
4
replies
2.1k
views
Differential Network analysis
wgcna scalefree networks scale free
updated 4.8 years ago by ▴ 40 • written 4.8 years ago by ▴ 30
2
votes
7
replies
8.7k
views
Samtools command not found
error
4.8 years ago by julianneradford ▴ 20
1
vote
7
replies
1.8k
views
Exprimental design for DESeq2 or edger
deseq2 edger
4.8 years ago by zizigolu ★ 4.4k
0
votes
0
replies
808
views
High Throughput Screening (HTS) Data Statistical Analysis R Package
High Throughput Screening Statistical Analysis
4.8 years ago by Hamidreza Hashemi • 0
0
votes
4
replies
1.0k
views
Question: should we integrate samples from different study groups?
RNA-Seq scRNA-seq
updated 4.8 years ago by 13k • written 4.8 years ago by • 0
4
votes
12
replies
4.1k
views
TMM normalized TPM
RNA-Seq
4.8 years ago by firestar ★ 1.7k
1
vote
0
replies
2.1k
views
Has anyone tried "star --readFilesManifest manifest.tsv" and then "featureCounts --byReadGroup" to quickly get gene quantification for multiple sampl…
RNA-Seq STAR featureCounts
4.8 years ago by Xianjun ▴ 310
2
votes
2
replies
2.1k
views
not able to run Fastqc in Centos server
fastqc genomics
updated 4.8 years ago by 20 • written 6.0 years ago by ▴ 1000
0
votes
0
replies
1.2k
views
Using DiffBind for ATACseq data with Multiple Conditions
diffbind ATAC-seq
4.8 years ago by blaura.bioinfo • 0
0
votes
3
replies
1.1k
views
Searching for Cell Type Database -- Similar to GeneCards
database
updated 4.8 years ago by 154k • written 4.8 years ago by ▴ 10
2
votes
2
replies
2.0k
views
Bowtie 2 warning when outputting unmapped reads
alignment bowtie2
updated 4.8 years ago by 90k • written 4.8 years ago by ▴ 10
0
votes
4
replies
2.7k
views
Understanding GATK evaluation metrics
next-gen snp GATK metrics
4.6 years ago by geneart$$ ▴ 50
0
votes
1
reply
1.1k
views
Hisat2 file error
RNA-Seq
updated 3.7 years ago by 45k • written 4.8 years ago by • 0
0
votes
8
replies
2.8k
views
Adding a gene to a GTF file
RNA-Seq
4.8 years ago by science_lizard ▴ 30
0
votes
0
replies
596
views
GO Enrichment Pichia pastoris
rna-seq gene_ontology GO_slim pichia pastoris
4.8 years ago by Adishi • 0
2
votes
5
replies
1.8k
views
bowtie2 mapping oritation problem
bowtie2 WGS DNA sequencing
updated 4.8 years ago by 35k • written 4.8 years ago by • 0
0
votes
4
replies
2.8k
views
Merge two vcf's, keep only intersection of REF/ALT alleles
vcf vcftools bcftools intersection merge
updated 3.9 years ago by ▴ 580 • written 4.8 years ago by • 0
4
votes
9
replies
11k
views
p.adjusted p value
r pvalue FDR RNA-Seq
updated 4.8 years ago by 90k • written 4.8 years ago by ▴ 160
1
vote
8
replies
2.8k
views
Beagle Conform-gt Java Error
Beagle Conform-gt Java Imputation topmed
updated 4.8 years ago by 154k • written 4.8 years ago by • 0
0
votes
0
replies
1.3k
views
Help with this error code for tool subset_taxa; Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
phyloseq biom subset_taxa Error in dimnames(x)
updated 4.8 years ago by 154k • written 4.8 years ago by • 0
0
votes
2
replies
1.3k
views
lncRNA identification from RNAseq data
lncrna rna RNA-Seq hisat2 stringtie
updated 4.8 years ago by 7.6k • written 4.8 years ago by ▴ 10
7
votes
3
replies
19k
views
Enrichment Score Interpretation
RNA-Seq R pathways gsea Enrichment
updated 15 months ago by ▴ 390 • written 4.8 years ago by ▴ 20
5
votes
4
replies
2.6k
views
Variant calling on RNA-Seq data
RNA-Seq SNP gene
updated 4.8 years ago by 4.2k • written 4.8 years ago by ▴ 10
0
votes
2
replies
1.2k
views
format problem(.beagle.gz files)
raxml
4.8 years ago by Daier ▴ 20
18
votes
12
replies
8.0k
views
Removal of repeat and blacklist regions from ChIP-seq data
ChIP-Seq Blacklist ENCODE
updated 4.8 years ago by 20 • written 8.8 years ago by ★ 3.5k
3
votes
3
replies
1.9k
views
Copy number variations from WES data
CNV WES
updated 4.8 years ago by ▴ 40 • written 4.8 years ago by ▴ 120
1
vote
1
reply
1.1k
views
why should we cluster cells when we can label them using databases, in single cell RNA-seq analysis?
RNA-Seq rna-seq
4.8 years ago by tbg ▴ 120
0
votes
1
reply
824
views
netmatch app crash
cytoscape netmatch
4.8 years ago by am.binder.ba • 0
0
votes
0
replies
934
views
GTEX Gene Selection
GTex
4.8 years ago by Nona ▴ 90
0
votes
0
replies
858
views
Programmatically determining sequence type (g., m., c., n.)
sequence type prefix genomic coding
4.8 years ago by mike.rightmire ▴ 20
2
votes
1
reply
660
views
Graphic of expression on BrainSeq, what is on Y?
SNP
updated 4.8 years ago by 22k • written 4.8 years ago by • 0
0
votes
4
replies
1.9k
views
bedtools intersect correct usage
genome
updated 4.8 years ago by ▴ 40 • written 4.8 years ago by ▴ 30
4
votes
7
replies
2.9k
views
Mapping rate troubles
RNA-Seq alignment salmon STAR SEQmonk
4.8 years ago by thomas58 ▴ 20
0
votes
5
replies
1.8k
views
Annotate peaks and G quadruplex
ChIP-Seq
updated 4.8 years ago by ▴ 40 • written 5.5 years ago by ▴ 10
1
vote
2
replies
1.7k
views
METABRIC sample IDs
METABRIC sample cancer mRNA ID
updated 2.3 years ago by ★ 90k • written 4.8 years ago by • 0
0
votes
5
replies
3.7k
views
Problem while using BPGA-Version-1.3 for pan bacterial genome analysis
genome software error next-gen gene
updated 4.8 years ago by • 0 • written 7.8 years ago by • 0
3
votes
4
replies
4.8k
views
GSEA pvalue output of 0.0. Can I make it more specific?
GSEA P-value
updated 4.8 years ago by ★ 1.0k • written 5.3 years ago by ▴ 300
2
votes
3
replies
5.8k
views
What Information Does The Encode Chip-Seq Peak File Contain
chip-seq encode
updated 4.8 years ago by 20 • written 14.5 years ago by ▴ 790
15
votes
2
replies
4.1k
views
Tool: EnhancedVolcano becomes a pseudo-EnhancedMA
enhancedMA enhancedvolcano
updated 2.5 years ago by 45k • written 5.3 years ago by ★ 90k
122,217 results • Page 720 of 2445
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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?
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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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