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370 results • Page
4 of 8
Sort: replies
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Votes
Replies
0
votes
3
replies
46
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
23 minutes ago by
WouterDeCoster
47k
0
votes
3
replies
472
views
Adding CB tag to bam file
samtools
bam
updated 3 days ago by
swbarnes2
14k • written 4 days ago by
Maria
• 0
3
votes
3
replies
450
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 3 days ago by
swbarnes2
14k • written 4 days ago by
joe
▴ 510
1
vote
3
replies
393
views
Limma compare between 3 conditions vs 2 conditions
Limma
updated 6 days ago by
Gordon Smyth
★ 7.0k • written 28 days ago by
Chris
▴ 260
3
votes
3
replies
402
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
6 days ago by
ayushm64
• 0
1
vote
3
replies
1.0k
views
problem with facing strange gene name in TCGA data
TCGA
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 5.6 years ago by
modarzi
▴ 170
6
votes
3
replies
150
views
Interpretting IGV output
IGV
updated 1 day ago by
Carlo Yague
8.7k • written 1 day ago by
analyst
▴ 20
1
vote
2
replies
248
views
Visualization of PROKKA Annotation Result?
PROKKA
Annotation
updated 6 days ago by
Joe
21k • written 8 days ago by
ferdinand
▴ 10
1
vote
2
replies
223
views
CombineGVCFs vs. MergeVcfs
CombineGVCFs
MergeVcfs
GATK
WGS
GVCF
updated 6 days ago by
Jeremy Leipzig
22k • written 7 days ago by
Sd
• 0
2
votes
2
replies
379
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
GEO
velocity
count-matrix
updated 6 days ago by
Ram
43k • written 7 days ago by
Spring
• 0
0
votes
2
replies
249
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 6 days ago by
Ram
43k • written 7 days ago by
David
• 0
4
votes
2
replies
267
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 6 days ago by
Ram
43k • written 6 days ago by
Adi
▴ 10
0
votes
2
replies
279
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
6 days ago by
Koketso
• 0
2
votes
2
replies
232
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 6 days ago by
bk11
★ 2.3k • written 6 days ago by
bgbs
• 0
1
vote
2
replies
257
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
6 days ago by
bioinfo
▴ 150
1
vote
2
replies
805
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 6 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 6 days ago by
Ram
43k • written 2.9 years ago by
Mat
▴ 60
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva
combat
batch-effect
DESeq2
updated 6 days ago by
Ram
43k • written 3.7 years ago by
svp
▴ 680
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma
Batch-effect
MDS
Galaxy
updated 6 days ago by
Ram
43k • written 4.8 years ago by
sonayuv
• 0
1
vote
2
replies
1.8k
views
Data processing order: normalisation or batch effect correction first?
limma
proteome
batch-effect
R
updated 6 days ago by
Ram
43k • written 3.5 years ago by
Sebastian Hesse
▴ 340
0
votes
2
replies
810
views
Is it correct to merge two raw CEL datasets and then perform quality control, background correction, and normalization on it?
R
microarray
affymetrix
batch-effect
quality-control
updated 6 days ago by
Ram
43k • written 2.9 years ago by
Sib
▴ 60
2
votes
2
replies
947
views
Is there a file information dictionary for files downloaded from ENCODE through batch download?
ENCODE
updated 6 days ago by
Ram
43k • written 4.6 years ago by
burcakotlu
▴ 40
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq
quantification
alignment
updated 6 days ago by
Ram
43k • written 5.1 years ago by
mohammedtoufiq91
▴ 250
1
vote
2
replies
4.6k
views
predict TF binding sites from DNA sequence
TF
TRANSFAC
TFBS
binding-site
updated 6 days ago by
Ram
43k • written 6.6 years ago by
grant.hovhannisyan
★ 2.6k
2
votes
2
replies
625
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 6 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
3
votes
2
replies
1.0k
views
Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
RNA-Seq
Cross-Species
SVA
ComBat
Batch-Effect
updated 6 days ago by
Ram
43k • written 4.6 years ago by
rodguinea
• 0
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect
DESeq2
miRNA-Seq
updated 6 days ago by
Ram
43k • written 5.5 years ago by
prekrish
• 0
3
votes
2
replies
806
views
Retrieve initial query in getBM()
getBM
biomaRt
R
gene
updated 6 days ago by
Ram
43k • written 3.2 years ago by
helia.ziaei
• 0
7
votes
2
replies
3.6k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 6 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
2
votes
2
replies
1.6k
views
How to add a title to a cnetplot?
r
cnetplot
updated 6 days ago by
Ram
43k • written 3.5 years ago by
appropiate
▴ 80
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios
Cox-model
survival
updated 6 days ago by
Ram
43k • written 4.3 years ago by
akutasame
▴ 40
1
vote
2
replies
1.4k
views
How to download a list pdb codes contained in a csv file using
Biopython
updated 6 days ago by
Ram
43k • written 3.1 years ago by
jmungar2
▴ 10
1
vote
2
replies
191
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
6 days ago by
hagl
▴ 10
0
votes
2
replies
235
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
6 days ago by
mropri
▴ 150
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 5 days ago by
Dr.Animo
▴ 130 • written 12 months ago by
BioinfoBee
• 0
0
votes
2
replies
228
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
5 days ago by
DKA
▴ 40
0
votes
2
replies
209
views
Bedmethyl file format
bedmethyl
methylation
updated 5 days ago by
GenoMax
141k • written 6 days ago by
njornet
▴ 20
1
vote
2
replies
327
views
Forum:
VCF bulk handling
bcftools
SnpEff
WGS
VEP
VCF
5 days ago by
Javier
• 0
0
votes
2
replies
360
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
5 days ago by
arriyaz.nstu
▴ 30
1
vote
2
replies
263
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 5 days ago by
Ram
43k • written 5 days ago by
aniigodwinn
• 0
0
votes
2
replies
1.3k
views
Interpretation problem at PCA plot for detecting batch effect
PCA
RNA-Seq
batch-effect
updated 5 days ago by
Ram
43k • written 4.4 years ago by
modarzi
▴ 170
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 5 days ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
0
votes
2
replies
2.9k
views
Should I pre-normalize RNAseq data before combat?
RNA-Seq
combat
batch-effect
R
updated 5 days ago by
Ram
43k • written 4.8 years ago by
zhaoliang0302
▴ 50
2
votes
2
replies
1.7k
views
Remove batch effect for many RNA-seq
ComBat
RNA-Seq
batch-effect
sva
updated 5 days ago by
Ram
43k • written 4.8 years ago by
Shaway
• 0
1
vote
2
replies
2.1k
views
RNA-seq unbalanced batch effect correction
RNA-Seq
edgeR
R
Batch-Effect
updated 5 days ago by
Ram
43k • written 5.6 years ago by
sckinta
▴ 730
0
votes
2
replies
360
views
How can I solve this error?
metal
5 days ago by
22211020193
• 0
0
votes
2
replies
298
views
GSEA analysis in R
GSEA
R
Arabidopsis
5 days ago by
Sudip
• 0
4
votes
2
replies
306
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 5 days ago by
Juke34
8.5k • written 5 days ago by
njornet
▴ 20
0
votes
2
replies
336
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 4 days ago by
Ehsan
• 0 • written 8 weeks ago by
bioinfo
▴ 150
2
votes
2
replies
366
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
4 days ago by
nhaus
▴ 300
370 results • Page
4 of 8
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Comment: Correlation for ATAC-Seq and Chip-Seq
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Comment: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
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Comment: Help for coding: Trinity for differential gene expression studies
by
rhossen
• 0
RSEM wiki is not working or there is no page for RSEM
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over
by
WouterDeCoster
47k
I want reads in a specific short interval, but if I do that with samtools view I also get reads that are spliced over that interval.
Answer: Help for coding: Trinity for differential gene expression studies
by
mchour
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Hello, I would recommend following RSEM wiki for more information about the options, or even run RSEM directly, not with the script provi…
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by
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54k
This seems like a model case for why we need better sustainable bioinformatics data and services. I don't know the exact background behind …
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this is names.dmp:![names.dmp][1] and nodes.dmp![nodes.dmp][2] [1]: /media/images/33cc9a8b-4818-48b4-913d-1c2b2185 [2]: /media/i…
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over
by
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161k
see also : https://www.biostars.org/p/9537698/ ; https://www.biostars.org/p/9464312/ ; https://www.biostars.org/p/417123/
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over
by
Pierre Lindenbaum
161k
what's the gray section ? it's the read you want ? do you only want the reads that end at the splice event (single point location) ?
Comment: interpretartion of a vcf file
by
Pierre Lindenbaum
161k
yes if there is more than one sample genotyped.
Comment: interpretartion of a vcf file
by
samuelkalandarov2002
▴ 10
Is it typical to observe such a profile in the context of diploid organism ?
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by
Basti
★ 2.0k
Yes you can use ggplot2 to create your own plots from a table of results from a differential methylation analysis. You just need to adapt a…
Comment: Heatmap and rna-seq
by
Basti
★ 2.0k
This forum is not dedicated to this type of request, there are many online tutorials for creating heatmaps accessible with simple internet …
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Download the CPC2 tool supported by python 3 from here [https://github.com/gao-lab/CPC2_standalone/releases/tag/v1.0.1][1]. Then follow …
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4.2k
let me know the scope and scale of the request (e.g. I need to do this for every record in Pubmed) and can help
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
how is this query itself originating?
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
I was able to come up with a workaround using the requests library: import requests pmid = 30134295 url = 'https://pubmed.ncbi…
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