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3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 6 days ago by 43k • written 7.1 years ago by ▴ 310
3
votes
3
replies
464
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 5 days ago by 14k • written 6 days ago by ▴ 510
2
votes
5
replies
430
views
Marking duplicates using UMIs
Deduplication UMI
updated 3 days ago by 19k • written 4 days ago by • 0
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 6 days ago by 43k • written 18 months ago by • 0
2
votes
7
replies
807
views
Removing duplicates
duplicates ONT minimap2
updated 6 days ago by ▴ 510 • written 8 days ago by • 0
2
votes
9
replies
807
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 1 day ago by 4.2k • written 6 months ago by • 0
2
votes
5
replies
678
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by ▴ 740 • written 5 days ago by ★ 2.4k
2
votes
4
replies
243
views
interpretartion of a vcf file
calling genotype ONT variant diploid
1 day ago by samuelkalandarov2002 ▴ 10
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq batch-effect sequencing
updated 6 days ago by 43k • written 6.9 years ago by • 0
1
vote
3
replies
193
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
2 days ago by WouterDeCoster 47k
1
vote
2
replies
160
views
alignment result
RNA-seq samtools hisat2
6 hours ago by ahmad.sajad4541 • 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor limma sva r batch-effect
updated 6 days ago by 43k • written 7.6 years ago by ★ 1.2k
1
vote
0
replies
537
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers TRINITY
5 days ago by mathavanbioinfo ▴ 90
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS exome-sequencing batch-effect
updated 6 days ago by 43k • written 6.5 years ago by ▴ 270
1
vote
3
replies
229
views
some error in building kraken2 database
metagenome kraken2
1 day ago by Art1ess • 0
1
vote
1
reply
412
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
updated 4 days ago by ★ 7.0k • written 6 days ago by ▴ 260
1
vote
1
reply
389
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
5 days ago by renan.igor • 0
1
vote
2
replies
226
views
permutation test in edgeR
rna-seq edgeR
updated 3 days ago by ★ 7.0k • written 17 days ago by • 0
1
vote
1
reply
157
views
Failed kmer content
kmer illumina ngs
updated 1 day ago by 43k • written 2 days ago by • 0
1
vote
5
replies
246
views
Downsampling fastq file
downsample fastq
updated 2 days ago by 43k • written 2 days ago by ▴ 80
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink PED
updated 2 days ago by 10k • written 6.1 years ago by ▴ 10
0
votes
1
reply
818
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR Batch-effect RNA-Seq
updated 6 days ago by 43k • written 3.7 years ago by • 0
0
votes
0
replies
176
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
5 days ago by DanielEB_fisk ▴ 20
0
votes
0
replies
731
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq scRNA-Seq batch-effect
updated 6 days ago by 43k • written 3.4 years ago by ▴ 180
0
votes
0
replies
192
views
miRDeep2: How to get the read counts
mirdeep2
6 days ago by Atul K. • 0
0
votes
4
replies
573
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
6 days ago by Kai Xin • 0
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression mirdeep2 miRNA
6 days ago by Ashok • 0
0
votes
2
replies
418
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control SNV QC SNP
5 days ago by _quantum_girl_ ▴ 10
0
votes
1
reply
280
views
Could you please assist in identifying this cluster?
single-cell
updated 5 days ago by 43k • written 5 days ago by • 0
0
votes
0
replies
193
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 5 days ago by 43k • written 6 days ago by • 0
0
votes
2
replies
372
views
error in coding potential calculator CPC2
cpc CPC2 coding-potential
6 days ago by Ashok • 0
0
votes
0
replies
1.9k
views
batch effect in radseq
radseq batch-effect SNP
updated 6 days ago by 43k • written 7.5 years ago by ▴ 50
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq batch-effect
updated 6 days ago by 43k • written 6.6 years ago by ▴ 80
0
votes
0
replies
175
views
Pruning with plink finds a majority of SNPs in very high LD
LD SNP plink pruning
6 days ago by enferdeflame • 0
0
votes
2
replies
532
views
How to get the reference panel for UKBB
UKBB GWAS clump
6 days ago by 航太郎 • 0
0
votes
0
replies
132
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation CGenFF Gromacs VMD
4 days ago by Mamatha Y S • 0
0
votes
0
replies
1.9k
views
Correcting batch effect from known variables in RnBeads using Combat
Combat 450k methylation RnBeads batch-effect
updated 6 days ago by 43k • written 7.1 years ago by ▴ 40
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 5 days ago by • 0 • written 6.5 years ago by ▴ 30
0
votes
0
replies
213
views
create genewise sync file in popoolation
popoolation
updated 6 days ago by 141k • written 6 days ago by • 0
0
votes
2
replies
537
views
autodockvina
python python3 autodock
updated 6 days ago by 43k • written 4 months ago by • 0
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma RNA-Seq edgeR batch-effect
updated 6 days ago by 43k • written 7.0 years ago by • 0
0
votes
0
replies
210
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
4 days ago by abhishekghadge • 0
0
votes
0
replies
185
views
agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 5 days ago by 43k • written 5 days ago by • 0
0
votes
0
replies
186
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
5 days ago by Nitin • 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria mauve genome
4 days ago by rthapa ▴ 90
0
votes
0
replies
187
views
absolute path for symbolic links in Snakefile
Snakemake
updated 5 days ago by 43k • written 5 days ago by ▴ 60
0
votes
0
replies
136
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 3 days ago by 43k • written 4 days ago by • 0
0
votes
2
replies
257
views
bam merging for archaic samples
samtools bam
updated 3 days ago by 43k • written 4 days ago by ▴ 100
0
votes
1
reply
259
views
Downloading the raw microarray data from GEO
.gpr microarray .CEL
updated 5 days ago by 141k • written 5 days ago by ▴ 10
0
votes
0
replies
1.8k
views
Differential expression using Scran batch corrected data
single-cell Batch-effect RNA-Seq Scran
updated 6 days ago by 43k • written 5.5 years ago by ▴ 10
109 results • Page 1 of 3
Recent Votes
discoSnp - reference-free finding of isolated SNPs from non assembled reads
Comment: Figures are disappeared from html report of SnpEff
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
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Recent Replies
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by GenoMax 141k
At this point you should email NCBI help desk and ask them this question. If you get an answer then please post it back in this thread.
Comment: Figures are disappeared from html report of SnpEff by Pierre Lindenbaum 161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff by analyst ▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data by Kazo • 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work? by Assa Yeroslaviz ★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error by Adrian Altenhoff ★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid by ashaneev07 ▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM by dsull ★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data by sehriban.buyukkilic ▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data by sehriban.buyukkilic ▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file by Pierre Lindenbaum 161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file by Maria • 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff by Pierre Lindenbaum 161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
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