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900 results • Page 6 of 18
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2
votes
0
replies
1.9k
views
ComBat-seq adjustment of batch effects
RNA-Seq ComBat-seq SVA edgeR batch-effect
updated 29 days ago by 43k • written 3.5 years ago by ▴ 50
2
votes
4
replies
372
views
SnpEff annotates coding duplication as intronic?
snpeff
29 days ago by kirill.zaslavsky • 0
2
votes
3
replies
321
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus annotation assembly genome
updated 12 days ago by ★ 2.0k • written 13 days ago by ▴ 30
2
votes
4
replies
389
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 22 days ago by 14k • written 23 days ago by • 0
2
votes
2
replies
347
views
Association study using SNP data
Association Allele Parentage SNP
10 days ago by drajangirija • 0
2
votes
3
replies
396
views
Editing Human Reference Genome by adding a CDS
gff agat transcriptome
updated 28 days ago by 54k • written 28 days ago by ▴ 340
2
votes
3
replies
201
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC RNA-Seq
updated 1 day ago by 43k • written 1 day ago by • 0
2
votes
3
replies
269
views
Finding variants within a subset of a BAM file
variant calling
1 day ago by ramiro.barrantes • 0
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 27 days ago by 43k • written 4.8 years ago by ▴ 20
2
votes
6
replies
367
views
BWA alignment
Samtools bam
updated 1 day ago by ▴ 260 • written 3 days ago by • 0
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq alignment RNA-Seq featureCounts STAR
updated 2 days ago by ▴ 340 • written 4.9 years ago by ▴ 70
2
votes
1
reply
328
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 12 days ago by 10k • written 15 days ago by ▴ 10
2
votes
2
replies
646
views
Batch correction for DE analysis
batch-correction mRNA RNA-seq DEGs MDSplot
updated 29 days ago by 43k • written 2.7 years ago by ▴ 10
2
votes
0
replies
154
views
News: course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics SNPs LocalAdaptation GIS
6 days ago by carlopecoraro2 ★ 2.5k
2
votes
2
replies
1.6k
views
Combining control samples from 2 separate studies. Model matrix for batch effect?
gene-expression R limma batch-effect model-matrix
updated 27 days ago by 43k • written 7.3 years ago by ▴ 20
2
votes
5
replies
783
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 25 days ago by ▴ 770 • written 26 days ago by ★ 2.4k
2
votes
3
replies
497
views
Sheep reference genome remapping coordinates
reference remap sheep coordinates genome
27 days ago by valentinatsar • 0
2
votes
3
replies
378
views
clustalo - align milions of short seq, memory issue
memory clustalo
updated 23 days ago by ★ 27k • written 23 days ago by ▴ 120
2
votes
5
replies
530
views
Marking duplicates using UMIs
Deduplication UMI
updated 23 days ago by 19k • written 25 days ago by • 0
2
votes
5
replies
562
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
29 days ago by Bikram Kumar • 0
2
votes
5
replies
1.9k
views
Differential Expression Analysis with batches which have different biological groups
R RNA-Seq limma DE batch-effect
updated 28 days ago by 43k • written 4.8 years ago by ▴ 60
2
votes
5
replies
631
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 25 days ago by ★ 27k • written 26 days ago by • 0
2
votes
1
reply
231
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 4 days ago by 161k • written 5 days ago by ▴ 70
2
votes
6
replies
1.8k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML ncbi entrez-direct
updated 10 hours ago by 43k • written 3.9 years ago by • 0
2
votes
5
replies
420
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
20 days ago by Lada ▴ 30
2
votes
2
replies
215
views
MA plot of shrunken fold change
MA-plot Deseq2
updated 16 days ago by 82k • written 16 days ago by • 0
2
votes
5
replies
255
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 2 days ago by 8.5k • written 2 days ago by • 0
2
votes
2
replies
303
views
p-value in CIBERSORT
CIBERSORT p-value
14 days ago by michelafrancesconi9 ▴ 20
2
votes
3
replies
388
views
How to establish haplotype-specific gene expression levels
RNA-seq Haplotype
updated 19 days ago by ★ 6.0k • written 5 weeks ago by ▴ 60
2
votes
2
replies
295
views
How to filter columns in a raw sparse matrix in R
matrix R
updated 29 days ago by ★ 2.4k • written 29 days ago by • 0
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 21 days ago by • 0 • written 2.5 years ago by • 0
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq batch-effect
updated 27 days ago by 43k • written 5.0 years ago by ▴ 60
2
votes
2
replies
426
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edgeR
27 days ago by nhaus ▴ 360
2
votes
3
replies
329
views
Problem with Seurat package in PercentageFeatureSet function
cell single
updated 6 days ago by ★ 2.4k • written 11 days ago by ▴ 60
2
votes
3
replies
840
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 11 days ago by • 0 • written 7 months ago by • 0
2
votes
4
replies
281
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
1 day ago by Esraa • 0
2
votes
2
replies
240
views
Raw counts using stringtie
stringtie RNA-seq
updated 12 days ago by 142k • written 12 days ago by • 0
2
votes
8
replies
359
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 3 days ago by 161k • written 3 days ago by ▴ 100
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 7 days ago by • 0 • written 5.1 years ago by ★ 1.8k
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 17 days ago by ★ 7.2k • written 8 months ago by ▴ 10
2
votes
5
replies
535
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
17 days ago by ashaneev07 ▴ 20
2
votes
3
replies
1.5k
views
RNASeq - How to compare the expression of a single gene across batches
RNA-Seq edgeR batch-effect
updated 27 days ago by 43k • written 3.6 years ago by ▴ 20
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by • 0 • written 4.8 years ago by ▴ 60
2
votes
2
replies
184
views
Is therer any suggestions on mapping rate of WGBS data?
mapping read alignment WGBS
8 days ago by Zeng Jingyu ▴ 60
2
votes
2
replies
190
views
Genome Visualization Tools
bacterial genome
updated 1 day ago by 142k • written 1 day ago by ▴ 10
2
votes
2
replies
248
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB protein STRING-DB-API
10 days ago by brandon • 0
2
votes
5
replies
2.9k
views
Batch effect in Axiom Human Origins Array
affymetrix array batch-effect
updated 29 days ago by 43k • written 7.9 years ago by ▴ 50
2
votes
5
replies
953
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 16 days ago by ★ 2.0k • written 2.1 years ago by • 0
1
vote
2
replies
268
views
RNA-seq data for deep learning classification
rna-seq
12 days ago by yahn • 0
1
vote
3
replies
3.4k
views
How to correct for batch effect in microarray meta-analysis
ComBat microarray meta-analysis batch-effect
updated 27 days ago by 43k • written 10.0 years ago by ▴ 120
900 results • Page 6 of 18
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Comment: PyWGCNA
PyWGCNA
Collect dispersed executable files and run them by using bingo.
A: ensembl gene id
A: How to deal with the case that one gene symbol matches multiple ensembl ids?
Answer: DESeq2 error
Answer: Using ggplotly in R
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Recent Replies
Comment: ggrepel function: geom_text_repel() by zx8754 11k
There is a dedicated package for this, see - https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html
Comment: Sam file Header problem by Pierre Lindenbaum 161k
-R "@RG\tID:sample\tSM:sample\tPL:Illumina" where is this '@RG' in the header anyway ? are you sure you're handling the correct fil…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Pierre Lindenbaum 161k
it looks like the same error.
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thankyou so much Andres for your reply. I think I got your point, just have a couple of quick questions to make it more clear . 1) I do n…
Comment: Duplicated reads (IDs) from nanopore sequencing by njornet ▴ 20
I've looked into it and one of the reads with a supplementary alignment has the representative alignment aligning to the + strand and being…
Answer: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script by kuttibiotech2009 ▴ 30
Hello friends, Thank you for your feedback. I understand that the post may not directly relate to bioinformatics. My aim was to share …
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
You do not merge the MEs. It is quite normal that some modules have noisy eigengenes (MEs); WGCNA is an unsupervised analysis overall. By …
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
my blast is latest version 2.15. I don't know what you want me to see in this link.
Answer: scRNAseq quality control weird double curve in nFeature vs nCount plot by valdirbarth ▴ 20
Is it possible that the cells that have their VDJ sequenced, those VDJ reads are not contributing to new genes detected? So you might be …
Comment: ggrepel function: geom_text_repel() by ntsopoul ▴ 60
The plot looks confusing, chek the documentation there is an attribute called force. If you reduce the value you should get better results.…
Comment: Sequencing Depth (Read Depth) Calculations by LucisTheFather • 0
Understood! Gonna try those two!
Comment: Sequencing Depth (Read Depth) Calculations by LucisTheFather • 0
Thank u very much!
Comment: How to extract cells of different species after mapping with combined genome? by GenoMax 142k
You have used the tag `snRNAseq`. I am not familiar with singleron tech but if you have sequence data you may be able to use `xenome` or `b…
Comment: bbmerge (bbmap) ~ error with insert size file output by GenoMax 142k
It may be best to go back to the original data and then do `bbmerge.sh` on it to get original insert size estimates (before any operations …
Comment: bbmerge (bbmap) ~ error with insert size file output by chrisk • 0
Hi Brian, Thank you and apologies for the extra future revision works. Out of curiosity we disabled neural networks 'nn=f' and the file o…
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