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924 results • Page
7 of 19
Sort: Votes
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Votes
Replies
2
votes
2
replies
288
views
p-value in CIBERSORT
CIBERSORT
p-value
9 days ago by
michelafrancesconi9
▴ 20
2
votes
0
replies
225
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
25 days ago by
Alexander
▴ 220
2
votes
4
replies
2.3k
views
Negative values after batch correction using removeBatchEffect from Limma
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 23 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
2
votes
2
replies
1.7k
views
How to add a title to a cnetplot?
r
cnetplot
updated 23 days ago by
Ram
43k • written 3.5 years ago by
appropiate
▴ 80
2
votes
3
replies
985
views
Method to detect genome doubling
CNV
genome doubling
updated 18 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
2
votes
2
replies
298
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 28 days ago by
ATpoint
82k • written 29 days ago by
Shicheng Guo
★ 9.4k
2
votes
1
reply
309
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 6 days ago by
chrchang523
10k • written 10 days ago by
8armed
▴ 10
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 23 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
2
votes
5
replies
537
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
23 days ago by
Bikram Kumar
• 0
2
votes
5
replies
505
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
12 days ago by
ashaneev07
▴ 20
2
votes
5
replies
940
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 11 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
1
vote
1
reply
204
views
Failed kmer content
kmer
illumina
ngs
updated 17 days ago by
Ram
43k • written 17 days ago by
Kasturi
• 0
1
vote
3
replies
402
views
Ensembl gene id conversion
biomart
ensembl
updated 24 days ago by
ATpoint
82k • written 26 days ago by
naveedhasan2000
• 0
1
vote
5
replies
346
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
7 days ago by
Riccardo
▴ 10
1
vote
5
replies
1.6k
views
How to correct unknown Batch effect?
PCA
gene-expression
DESeq2
RNA-seq
batch-effect
updated 23 days ago by
Ram
43k • written 12 months ago by
luffy
▴ 110
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 23 days ago by
Ram
43k • written 6.3 years ago by
jjrin
▴ 40
1
vote
1
reply
293
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 20 days ago by
Gordon Smyth
★ 7.1k • written 20 days ago by
Bioinformatician
• 0
1
vote
3
replies
1.0k
views
problem with facing strange gene name in TCGA data
TCGA
RNA-Seq
batch-effect
updated 23 days ago by
Ram
43k • written 5.7 years ago by
modarzi
▴ 170
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
8 days ago by
eebloom
▴ 80
1
vote
5
replies
648
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 20 days ago by
GenoMax
142k • written 21 days ago by
Luka
• 0
1
vote
4
replies
360
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
2 days ago by
heelpPlease
• 0
1
vote
0
replies
142
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
4 days ago by
Biostar
2.7k
1
vote
2
replies
305
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
3 days ago by
M.
▴ 30
1
vote
3
replies
503
views
how to get the variance explained by the independent variable from multivariate distance matrix regression model with random effect?
multivariate-distance-matrix
regression
updated 24 days ago by
LChart
3.9k • written 25 days ago by
leranwangcs
▴ 120
1
vote
2
replies
180
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 1 day ago by
Michael
54k • written 1 day ago by
ashaneev07
▴ 20
1
vote
3
replies
284
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
17 days ago by
WouterDeCoster
47k
1
vote
3
replies
423
views
PCA plot
DESeq2
PCAplot
updated 12 days ago by
LauferVA
4.2k • written 15 days ago by
Aaliya
▴ 10
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 26 days ago by
Aspire
▴ 330 • written 19 months ago by
Manav
• 0
1
vote
2
replies
178
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
2 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
398
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
22 days ago by
otieno43
▴ 30
1
vote
1
reply
237
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 16 days ago by
Pierre Lindenbaum
161k • written 16 days ago by
Biostar
2.7k
1
vote
3
replies
215
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 1 day ago by
GenoMax
142k • written 1 day ago by
cput
• 0
1
vote
1
reply
128
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 1 day ago by
andres.firrincieli
3.6k • written 1 day ago by
kacollier
▴ 30
1
vote
2
replies
226
views
Finding variants within a subset of a BAM file
variant
calling
updated 29 days ago by
Pierre Lindenbaum
161k • written 29 days ago by
ramiro.barrantes
• 0
1
vote
0
replies
125
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
sarumonsus
▴ 10
1
vote
10
replies
1.0k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
15 days ago by
DKA
▴ 40
1
vote
10
replies
861
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 4 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
1
vote
1
reply
251
views
Seurat V5 integration
Seurat
integration
updated 1 day ago by
Ram
43k • written 5 days ago by
starswillfade
▴ 10
1
vote
2
replies
247
views
RNA-seq data for deep learning classification
rna-seq
7 days ago by
yahn
• 0
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva
svaseq
batch-effect
updated 22 days ago by
Ram
43k • written 6.9 years ago by
wamiqsaifi
• 0
1
vote
5
replies
406
views
HCL database download
HCL
updated 2 days ago by
Ram
43k • written 6 days ago by
sooni
▴ 20
1
vote
2
replies
4.6k
views
predict TF binding sites from DNA sequence
TF
TRANSFAC
TFBS
binding-site
updated 23 days ago by
Ram
43k • written 6.7 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
2
replies
163
views
Where to get the following bed file?
WES
bed
reference
file
updated 3 days ago by
GenoMax
142k • written 3 days ago by
wyuan37
• 0
1
vote
1
reply
279
views
How to handle more than 1 SRA Run per Experiment?
SRA
Preprocessing
updated 27 days ago by
ATpoint
82k • written 27 days ago by
Janmajay
• 0
1
vote
1
reply
202
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 24 days ago by
dsull
★ 6.0k • written 24 days ago by
niruf
• 0
1
vote
4
replies
3.2k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 22 days ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
1
vote
3
replies
348
views
Merging vcf files with bcftools ([E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?)
vcf
tabix
bcftools
updated 23 days ago by
Pierre Lindenbaum
161k • written 29 days ago by
giulia.cosenza
• 0
1
vote
4
replies
1.3k
views
Comparing RNA-Seq data to online databases
RNA-Seq
batch-effect
updated 23 days ago by
Ram
43k • written 4.7 years ago by
Victoria
▴ 10
1
vote
1
reply
246
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 10 days ago by
Michael
54k • written 10 days ago by
Lissa Cruz Saavedra
• 0
1
vote
5
replies
383
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 4 days ago by
Ram
43k • written 5 days ago by
snajafy
• 0
924 results • Page
7 of 19
Recent Votes
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Answer: Server or aws cloud- which one is better for gatk pipeline
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Comment: Question about methylation location
Comment: Question about methylation location
How to use minimap2?
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Recent Replies
Comment: In IGV is this a heterogeneous mutation or false call?
by
Pierre Lindenbaum
161k
> RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sound stupid but does this make sense to what I've previousl…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
When click the blat it brings me to chr19 and mentions the RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sou…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for that! I'll try and have a look and see what is amiss if I can... In your opinion what do you feel is wrong in my alignment from…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Pierre Lindenbaum
161k
yeah.. look at that, there is something wrong in your alignment, many reads were mapped in a location but they are all clipped, so somethin…
Comment: Custom Reference panel creation for data imputation from .vcf files
by
analyst
▴ 50
Hi [Kevin][1]! I have 80 samples of GBS data. I have called variants through GATK pipeline. Now I have to perform imputation. Do I need …
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Ah I've just found 'show soft clipped bases' and this is what comes up... how come it is all greyed out? ![enter image description here][…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
I've just displayed clipped bases and this is what it shows. Does this look right? ![enter image description here][1] ![enter imag…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Hi, I really appreciate you taking the time to reply. I'm still learning with IGV and sorry to sound very inexperienced but how would I che…
Answer: In IGV is this a heterogeneous mutation or false call?
by
Pierre Lindenbaum
161k
there is a clear shift in the depth just close to this mutation, you should set IGV to display the clipped bases + check if there is a DUP …
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
Using fastp, I found that the adapter sequence for the forward read is corresponding to Trans2_rc in the NexteraPE-PE.fa, while for the re…
Comment: cellranger error message
by
Max
• 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Giulio Genovese
▴ 390
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
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: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Pierre Lindenbaum
161k
I think this is useless, in the gatk doc: > For each variant, the tool will look for the target coordinate, reverse-complement and left-al…
Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
142k
Ideally you will know which adapters to use but if you don't then programs like `fastp` can auto-detect them. You could also use `bbduk.sh`…
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