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503 results • Page
3 of 11
Sort: Views
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Views
Votes
Replies
0
votes
1
reply
650
views
How to find the co ordinates of long reads (simulated by Badreads) with respect to the reference genome
long-reads
reference-genome
assembly
updated 12 days ago by
Ram
43k • written 2.7 years ago by
Ashi
▴ 20
0
votes
1
reply
649
views
How to fix FreeBayes error "unable to find FASTA index entry for bed files"
freebayes
variant-calling
RNA-Seq
updated 15 days ago by
Ram
43k • written 12 months ago by
wlei091226
• 0
0
votes
0
replies
646
views
METAL GWAS
allele-frequency
gwas
updated 15 days ago by
Ram
43k • written 2.4 years ago by
晗颖
• 0
8
votes
10
replies
639
views
bash script
whole-genome-sequencing
updated 2 days ago by
Ram
43k • written 9 days ago by
bestone
▴ 30
2
votes
2
replies
623
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 1 day ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
2
votes
6
replies
618
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 15 days ago by
Ram
43k • written 4 months ago by
zea
• 0
1
vote
2
replies
617
views
Nanopore multisample variant calling
SNPs
nanopore
SNP-calling
variants
multisample
19 days ago by
colindaven
6.3k
0
votes
0
replies
613
views
I performed Homer's annotatePeaks.pl on multiple tissues, yet when I run annotatePeaks on the merged tissues, I get fewer total annotated peaks. Is t…
Homer
ATACseq
18 days ago by
Ronin
• 0
0
votes
6
replies
605
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression
RNA-Seq
ONT
Nanopore
updated 8 days ago by
Ram
43k • written 4 months ago by
tw_140
• 0
0
votes
2
replies
604
views
Seeking Alternative Tools for Predicting Mature microRNAs from Vertebrate Animal Precursors in In Silico Study
mirdeep2
maturebayes
microrna
updated 15 days ago by
Ram
43k • written 12 months ago by
Beatriz
• 0
1
vote
1
reply
593
views
accessing the global gut microbial gene catalogue (MEDUSA)
medusa
gene-catalogue
gut-microbiome
updated 6 days ago by
Ram
43k • written 3.2 years ago by
ramin.k2013
• 0
0
votes
3
replies
589
views
Not all variants are annotated with AF - expected or a problem?
Variant-Calling
WGS
Alignment
updated 15 days ago by
Ram
43k • written 7 months ago by
Luiz
▴ 30
0
votes
0
replies
584
views
Avoid genome circularization with Canu assembler
circularization
ONT
Canu
repetitive-regions
assembler
updated 12 days ago by
Ram
43k • written 2.9 years ago by
Maria
• 0
0
votes
10
replies
579
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
16 days ago by
dzisis1986
▴ 70
1
vote
2
replies
573
views
Applicability of the SoupX ambient mRNA decontamination technique to fixed and/or multiplexed scRNAseq experiments
SoupX
scRNA-seq
28 days ago by
e.r.zakiev
▴ 190
0
votes
2
replies
571
views
Bacterial contamination in human DNA sample
Long-read-sequencing
Bacterial-contamination
updated 12 days ago by
Ram
43k • written 21 months ago by
priya.bmg
▴ 60
0
votes
3
replies
553
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
20 days ago by
Nitin
• 0
0
votes
1
reply
543
views
Differential Expression Analysis for miRNA
limma
Differential-gene-Expression
miRNA
updated 8 days ago by
Ram
43k • written 2.9 years ago by
Al
• 0
4
votes
9
replies
540
views
variant calling
variant-calling
updated 14 days ago by
Ram
43k • written 15 days ago by
dalibenam64
• 0
4
votes
7
replies
538
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
updated 15 days ago by
cmdcolin
★ 3.8k • written 19 days ago by
I0110
▴ 140
0
votes
9
replies
536
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 6 days ago by
LauferVA
4.2k • written 7 days ago by
Aki
▴ 10
1
vote
1
reply
534
views
GEO analysis with R
R
updated 15 days ago by
Ram
43k • written 2.3 years ago by
abdalla.m
• 0
4
votes
7
replies
516
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 4 days ago by
Ram
43k • written 5 days ago by
AHerik
▴ 20
0
votes
1
reply
509
views
Geneious vs Perl script of IN SILICO PCR
PCR
Geneious
updated 15 days ago by
Ram
43k • written 22 months ago by
Bio_Crap
• 0
2
votes
6
replies
505
views
Need help understanding core SNPs
SNPs
snippy
23 days ago by
ujichu
• 0
0
votes
2
replies
502
views
Gene expression assay Yeast sample prep
Live-cells
updated 15 days ago by
Ram
43k • written 22 months ago by
dshdixit
▴ 10
0
votes
6
replies
498
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
2 days ago by
Dunois
★ 2.5k
0
votes
8
replies
497
views
STAR aligner options
STAR
20 days ago by
theophile
• 0
1
vote
6
replies
495
views
Quest about the input data for PCA analysis
PCA
25 days ago by
tujuchuanli
▴ 100
0
votes
5
replies
474
views
How to assure that sequence consensus is genuine?
genome
11 days ago by
marongiu.luigi
▴ 710
3
votes
12
replies
472
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
15 days ago by
Lila M
★ 1.2k
0
votes
5
replies
471
views
seg fault, core dumped with manta 1.6.0
manta
gdb
updated 9 days ago by
Ram
43k • written 13 days ago by
Greg
• 0
1
vote
1
reply
465
views
Manta: What does all this mean
manta
Variant-calling
VEP
updated 15 days ago by
Ram
43k • written 8 months ago by
josh.mannheimer
• 0
0
votes
0
replies
463
views
How to map Uniref90 genes (IDs) to Antibiotic resistant genes databases?
CARD
metagenomics
Humann2
antibiotic-resistant-genes
uniref
updated 6 days ago by
Ram
43k • written 2.0 years ago by
ramin.k2013
• 0
0
votes
5
replies
459
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
26 days ago by
Learner
• 0
0
votes
9
replies
458
views
Low number of both surviving reads after trimming
trimmomatic
trimming
20 days ago by
Jay
• 0
1
vote
5
replies
453
views
Haddock 2.4
Protein
Docking
updated 28 days ago by
dthorbur
★ 1.9k • written 4 weeks ago by
Preeti
• 0
0
votes
1
reply
446
views
principal coordinate analysis
PCoA
R
updated 15 days ago by
Ram
43k • written 10 months ago by
rene.j.erhardt
▴ 20
1
vote
1
reply
445
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 9 days ago by
chrchang523
10k • written 9 days ago by
dsbusiness135
▴ 10
0
votes
6
replies
441
views
Download Panther entry list
PANTHER
27 days ago by
Nicolas
• 0
0
votes
0
replies
438
views
Tools for identifying trans-splicing from long read data
long-read
splicing
nanopore
trans-splicing
updated 12 days ago by
Ram
43k • written 13 months ago by
dthorbur
★ 1.9k
0
votes
6
replies
434
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
7 days ago by
marongiu.luigi
▴ 710
0
votes
3
replies
433
views
How do I get the gene annotations as a text file from a genbank file?
sequence-annotation
genbank
updated 19 days ago by
Ram
43k • written 19 days ago by
eae6d2e7
• 0
1
vote
1
reply
406
views
Long reads Annotation
long-reads
pacbio
updated 12 days ago by
Ram
43k • written 2.1 years ago by
Gerardo
• 0
0
votes
0
replies
405
views
Pairwise alignment of two long chromosomes (~100Mbp) with lastz
lastz
alignment
updated 12 days ago by
Ram
43k • written 20 months ago by
vahe.galstyan
• 0
0
votes
5
replies
400
views
Error running local blastn in R using system2
blastn
NCBI
R
19 days ago by
Harrison
• 0
0
votes
7
replies
389
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 21 days ago by
GenoMax
141k • written 21 days ago by
Patadu94
• 0
3
votes
5
replies
389
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
updated 14 days ago by
GenoMax
141k • written 15 days ago by
e.r.zakiev
▴ 190
0
votes
4
replies
386
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
20 days ago by
BRENO
• 0
0
votes
0
replies
385
views
BETA whether on the same scale when performing rank-based inverse normal transformation on the same type of phenotype data for two cohorts separately…
normal
inverse
transformation
6 days ago by
Isaac
• 0
503 results • Page
3 of 11
Recent Votes
High fold change values
C: Bcftools Mpileup Removes Marked Duplicates?
Prediction tools summary - zero values
A: Error with Formatdb of legacy blast?
Error with Formatdb of legacy blast?
Answer: How to convert SAM/BAM file to GTF/GFF file?
A: Ribo-seq vs RNA-seq read count
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Recent Replies
Comment: Removing duplicates
by
joe
▴ 490
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis
by
geneontologyhelp
▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data?
by
etiennedanis
▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates
by
joe
▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together?
by
GenoMax
141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
swbarnes2
14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates
by
quentinperriere
• 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
Answer: Inconsistency in SNP detection pipelines for multi-sample analysis
by
LChart
3.9k
> To replicate GVCF behavior and avoid issues with 0/0 genotypes appearing as missing, I don't use the -v option I'm not sure what you m…
Comment: Supergnova stuck in tutorial
by
GenoMax
141k
Your best option may be to email the author (and/or the senior author from the paper). Let them know that the FTP links mentioned on GitHub…
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
BioinfGuru
★ 1.7k
Thanks @lchart, I accept that, I'll wait to see if there's any more who want to input and then accept the answer
Comment: Per base sequence content failed miserably
by
GenoMax
141k
What kind of data is this? Plain genomic/amplicons? How you proceed will largely depend on the context. Can you also post the original fast…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
I guess the enlightening question is: duplicates of what?
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
LChart
3.9k
I don't think this approach will give you what you want. Combining multiple tissues in the way you are suggesting will result in a positive…
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