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1,000 results • Page 5 of 20
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8
votes
5
replies
5.2k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by ▴ 60
1
vote
5
replies
1.1k
views
Align short sequence against ONT reads
long-reads ONT alignment genome
updated 21 days ago by 43k • written 22 months ago by ▴ 40
0
votes
5
replies
1.6k
views
what does mean this error ? "(ERR): hisat2-align exited with value 1" in mapping long noncoding RNAs
long-non-coding-RNA lncRNA
updated 21 days ago by 43k • written 2.6 years ago by • 0
1
vote
5
replies
332
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
3 days ago by anasjamshed ▴ 120
0
votes
5
replies
421
views
How to build ribosomal interval files to use in CollectRnaSeqMetrics for hg38.p14
hg38.p14 ribosomal-intervals
updated 22 days ago by ▴ 510 • written 24 days ago by • 0
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq tophat batch-effect cufflinks
updated 9 days ago by 43k • written 5.3 years ago by • 0
2
votes
5
replies
284
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
1 day ago by Lada ▴ 30
3
votes
5
replies
271
views
Per base sequence content error in RNAseq analysis
RNA-seq analysis
updated 4 days ago by 141k • written 5 days ago by • 0
0
votes
5
replies
493
views
Is it possible to set different tracks to the same scale in JBrowse
track jbrowse
updated 14 days ago by 43k • written 16 days ago by • 0
5
votes
5
replies
850
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 14 days ago by 43k • written 10 months ago by ▴ 30
2
votes
5
replies
453
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
10 days ago by Bikram Kumar • 0
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 16 days ago by • 0 • written 3.8 years ago by ★ 1.8k
0
votes
5
replies
301
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 1 day ago by 141k • written 2 days ago by ▴ 90
0
votes
5
replies
402
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 16 days ago by 141k • written 17 days ago by • 0
3
votes
5
replies
410
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 23 days ago by 141k • written 24 days ago by ▴ 200
1
vote
5
replies
703
views
RNA seq differential expression analysis
RNA-seq normalization
updated 7 days ago by ★ 1.7k • written 9 days ago by • 0
0
votes
5
replies
335
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate BUSCO.
updated 22 days ago by 141k • written 22 days ago by ▴ 10
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 11 days ago by ▴ 200 • written 16 months ago by ★ 1.4k
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq countOverlaps R
updated 10 days ago by 43k • written 6.3 years ago by ★ 1.9k
1
vote
5
replies
1.5k
views
Blastn in galaxy
Blastn galaxy
updated 24 days ago by 43k • written 3.0 years ago by • 0
1
vote
5
replies
562
views
Duplicate marking, read names, and the SRA
SRA MarkDuplicates
updated 7 days ago by 141k • written 7 days ago by • 0
2
votes
5
replies
483
views
Creating an index from multiple .fsa files
HISAT2 BWA Alignment
18 days ago by theworldsagainstme • 0
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA qRT-PCR R targeted-assay Batch-Effect
updated 11 days ago by 43k • written 3.9 years ago by ▴ 250
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis edgeR batch-effect DE
updated 9 days ago by 43k • written 5.1 years ago by ★ 1.9k
0
votes
5
replies
874
views
extraction of spanning long reads
long-reads
updated 21 days ago by 43k • written 17 months ago by ▴ 110
0
votes
5
replies
303
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
2 days ago by njornet ▴ 20
3
votes
5
replies
1.4k
views
Removing Batch effect that is the same as condition - DESEq2
RNA-Seq batch-effect DESeq2
updated 18 days ago by 43k • written 3.9 years ago by • 0
2
votes
5
replies
2.8k
views
Batch effect in Axiom Human Origins Array
affymetrix array batch-effect
updated 10 days ago by 43k • written 7.9 years ago by ▴ 50
5
votes
5
replies
543
views
NCBI MEGABLAST versus UCSC BLAT
blast blat alignment megablast
updated 17 days ago by ▴ 510 • written 18 days ago by ▴ 40
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R RNA-seq edgeR
updated 16 days ago by ▴ 60 • written 2.9 years ago by ★ 1.0k
3
votes
5
replies
1.3k
views
How to identify antibiotic resistant genes in gene databases?
antibiotic Gene-Ontology GO
updated 15 days ago by 43k • written 2.0 years ago by • 0
1
vote
5
replies
275
views
Downsampling fastq file
downsample fastq
updated 4 days ago by 43k • written 4 days ago by ▴ 80
2
votes
5
replies
1000
views
Ties in reranked list
fgsea GSEA
updated 13 days ago by • 0 • written 7 months ago by • 0
2
votes
5
replies
671
views
samtools mpileup taking too long
Bam samtools sam alignment
updated 21 days ago by 43k • written 6 weeks ago by • 0
0
votes
5
replies
1.2k
views
RNAseq differential gene expression analysis yield results which come from digestive content
differential-gene-expression RNA-Seq
updated 17 days ago by 43k • written 6.4 years ago by ▴ 90
3
votes
5
replies
1.3k
views
NextGen Sequencing Folks, what do you keep as your raw backup? BCL's or FASTQ's? Both?
next-gen-sequencing backups data-storage
updated 21 days ago by 43k • written 2.1 years ago by ▴ 130
1
vote
5
replies
371
views
Best way to deal with overlapping read names in merged BAM files
picard MarkDuplicates
11 days ago by shpak.max ▴ 50
2
votes
5
replies
453
views
Marking duplicates using UMIs
Deduplication UMI
updated 5 days ago by 19k • written 6 days ago by • 0
0
votes
5
replies
384
views
Parsing fasta file by coordinates
linux fasta
updated 29 days ago by 141k • written 4 weeks ago by ▴ 120
0
votes
5
replies
601
views
How to deeply sequence long inserts
Long-read phage NGS
updated 21 days ago by 43k • written 5 months ago by • 0
3
votes
5
replies
475
views
Having trouble building VG in Ubuntu
vg
updated 13 days ago by 43k • written 15 days ago by • 0
0
votes
5
replies
292
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 22 days ago by 43k • written 25 days ago by ▴ 150
0
votes
5
replies
335
views
Incongruencies in GT assignment by Freebayes
depth freebayes heterozygous genotype
21 days ago by virginia.baraja • 0
2
votes
5
replies
340
views
Tool to Identify Gene, Regulatory Role, and Function at Integration Sites
chromosome regulatory integration
updated 22 days ago by 161k • written 23 days ago by • 0
0
votes
5
replies
2.1k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq batch-effect normalization
updated 10 days ago by 43k • written 20 months ago by ▴ 60
9
votes
5
replies
2.2k
views
Millions of Reads Needed for Differential Gene Expression
differential-gene-expression RNA-Seq deseq2
updated 17 days ago by 43k • written 4.6 years ago by ▴ 20
2
votes
5
replies
2.3k
views
DGE on transcriptomic data, focus on transcript sequences or in derivated ORFs?
differential-gene-expression RNA-Seq ORFs
updated 17 days ago by 43k • written 6.4 years ago by ▴ 90
1
vote
5
replies
2.3k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 15 days ago by 82k • written 5.0 years ago by ▴ 750
0
votes
5
replies
425
views
Error running local blastn in R using system2
blastn NCBI R
28 days ago by Harrison • 0
3
votes
5
replies
551
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
5 days ago by n_navy • 0
1,000 results • Page 5 of 20
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Answer: Heatmap and rna-seq
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Comment: ScRNA data question by starswillfade ▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling by zihanss • 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
Comment: Correct way to compare multiple treaments between RNA-Seq samples using edgeR? by Guille • 0
Thank you for your answer! The MDS plot seems to group most treatment groups close-by, so I'm starting to suspect the effect of treatment …
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by Mensur Dlakic ★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq by dsull ★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708) by Gordon Smyth ★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR? by Gordon Smyth ★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu by Gordon Smyth ★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing by cao510927 ▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Alex Reynolds 35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data by bk11 ★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq by GenoMax 141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq by dsull ★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
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