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310 results • Page
2 of 7
Sort: Votes
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Votes
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1
vote
0
replies
146
views
Reducing BWA mem seed length when a genome is highly heterozygous?
alignment
bwa
17 days ago by
Axzd
▴ 10
1
vote
2
replies
233
views
Understanding TCGA barcodes with dot in the fieldname
tcga
updated 1 day ago by
Zhenyu Zhang
▴ 980 • written 4 days ago by
Tahsin
• 0
1
vote
2
replies
423
views
Ranked fold changes for non-replicated data
expression
metagenomics
LogFC
fold-change
updated 11 days ago by
Ram
40k • written 18 months ago by
Tom
▴ 540
1
vote
2
replies
273
views
Dotplot error: subscript out of bound
R
scRNA-seq
seurat
3 days ago by
Xuhao
• 0
1
vote
2
replies
310
views
Converting scMultiome data to loom using SEURAT
scMultiome
CCAF
Seurat
18 days ago by
halimaakhter014
• 0
1
vote
5
replies
260
views
Enrichment of mitochondrial and ribosomal pathways - an artifact?
Pathway
Mitochondria
Ribosome
scRNA-seq
Enrichment
21 hours ago by
omer.shomrat
• 0
1
vote
2
replies
233
views
Searching a tool to modify annotation files.
annotation
updated 16 days ago by
GenoMax
134k • written 16 days ago by
Charles Plessy
★ 2.9k
1
vote
1
reply
208
views
Inclusive vs. Separate Approaches for Gene Ontology Enrichment Analysis
Gene-Ontology
GO-terms
Enrichment
updated 28 days ago by
rfran010
▴ 810 • written 28 days ago by
Biomed-jeh
• 0
1
vote
0
replies
428
views
logFoldChange computed by EdgeR different from naive log2FCcomputed based on reads
edgeR
fold-change
updated 11 days ago by
Ram
40k • written 2.4 years ago by
ZheFrench
▴ 520
1
vote
0
replies
142
views
Genes in open chromatin region
ATAC-seq
DiffBind
11 days ago by
Chris
▴ 180
1
vote
1
reply
233
views
Single-end strand specific Rna-Seq: Which strand that the reads from.
mRNA
Single-end
strand-specific
TruSeq
updated 28 days ago by
mark.ziemann
★ 1.8k • written 4 weeks ago by
Chilly
▴ 10
1
vote
1
reply
984
views
SCENIC-openloom not working
sc-rna
SCENIC
sequencing
updated 2 days ago by
kyriakds
• 0 • written 2.1 years ago by
Lekshmy
▴ 10
1
vote
2
replies
288
views
functional analysis prediction
functionalanalysis
metabarcoding
16S
9 days ago by
safeassli
• 0
1
vote
3
replies
229
views
Finding sequences in unannotated genomes using reference coordinates
consensus
VCF
updated 4 days ago by
Ram
40k • written 5 days ago by
Prangan
▴ 20
1
vote
1
reply
246
views
Bioconductor Package Installation
bioconductor
updated 12 days ago by
Ram
40k • written 12 days ago by
oduduabasi.isaiah
• 0
1
vote
2
replies
223
views
Problem with Mageck paired analysis
Mageck
updated 15 days ago by
Meisam
▴ 200 • written 15 days ago by
toma.85
• 0
1
vote
4
replies
314
views
htseq-count reports count values for deleted genes
rna-seq
htseq
15 days ago by
kmyers2
▴ 80
1
vote
3
replies
673
views
How to determine plasmid or chromosomal origin?
plasmid
chromosomal-origin
updated 5 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
1
vote
5
replies
354
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 1 day ago by
ATpoint
77k • written 5 days ago by
vk
▴ 40
1
vote
11
replies
762
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 2 days ago by
GenoMax
134k • written 4 weeks ago by
langziv
▴ 50
1
vote
3
replies
299
views
Requesting further clarification on interpreting relative gene expression strength
R
normalization
TPM
RNA-seq
DESeq2
updated 13 days ago by
ATpoint
77k • written 27 days ago by
Abhishek
• 0
1
vote
5
replies
955
views
What statistical test to apply for DE after CibersortX deconvolution
cibersortx
differential-expression
t-test
deconvolution
15 days ago by
Sam
▴ 290
1
vote
1
reply
268
views
Which reference genome, DNA or cDNA and why?
or
DNA
cDNA
updated 23 days ago by
GenoMax
134k • written 24 days ago by
وفاء
• 0
1
vote
2
replies
272
views
Multiple testing adjustment for stepwise model selection
statistics
9 days ago by
mel22
▴ 100
1
vote
4
replies
300
views
rRNA filtering from human RNA-seq data
rRNA
RNA-seq
7 days ago by
deniz
▴ 10
1
vote
1
reply
731
views
GO enrichment and KEGG output empty
enrichment
GO
KEGG
clusterprofiler
NCBI
updated 28 days ago by
cardon.chc
• 0 • written 24 months ago by
estpallag
▴ 10
1
vote
5
replies
178
views
bcftools error merging two VCFs: REF prefixes differ
bcftools
VCF
14 hours ago by
Shane
• 0
1
vote
10
replies
900
views
Deepvariant variant calling by singularity
deepvariant
singularity
conda
docker
updated 4 days ago by
jeffhsu3
• 0 • written 12 weeks ago by
fra.silvestro99
▴ 10
1
vote
3
replies
277
views
Question regarding MACS2 approach of peak calling
MACS2
sequencing-depth
chipseq
updated 7 days ago by
ATpoint
77k • written 15 days ago by
rkc5
• 0
1
vote
3
replies
648
views
What are the definitions of the BBMerge outinsert table file?
bbmerge
outinsert
updated 29 days ago by
Dave Carlson
★ 1.4k • written 2.9 years ago by
Tawny
▴ 180
1
vote
0
replies
324
views
Strand orientation and GC skew
CGView
strand-orientation
GC-skew
updated 5 days ago by
Ram
40k • written 13 months ago by
A_heath
▴ 140
1
vote
5
replies
668
views
Mugsy percentage of identity
Mugsy
Genome-alignment
updated 5 days ago by
Ram
40k • written 2.5 years ago by
A_heath
▴ 140
1
vote
1
reply
240
views
GISTIC CNV
Gistic
updated 18 days ago by
Ram
40k • written 19 days ago by
ananta.kapoor
• 0
1
vote
4
replies
312
views
Gene expression
RNA-seq
DESeq2
Heatmap
updated 21 days ago by
ATpoint
77k • written 21 days ago by
Ralph
• 0
1
vote
3
replies
242
views
Sub-sampleing bam files based on sequencing_summary.txt (guppy output)
samtools
guppy
updated 6 days ago by
GenoMax
134k • written 6 days ago by
anika.john
• 0
1
vote
4
replies
398
views
How to understand if a GWAS sample comes from Chromosome X or Y
python
26 days ago by
dzisis1986
▴ 60
0
votes
1
reply
247
views
How to predict/annotate whether some type strains has a certain type of enzyme?
genome
gene
blast
annotation
updated 18 days ago by
GenoMax
134k • written 18 days ago by
JyiYeung
• 0
0
votes
3
replies
283
views
Assigning GO ids to blast hits
Linux
GO
blast
updated 1 day ago by
gv
• 0 • written 20 days ago by
Mousumi Akter
• 0
0
votes
2
replies
1.5k
views
Question about REDItools
REDItools
updated 11 days ago by
Ethan Lee
• 0 • written 4.1 years ago by
tujuchuanli
▴ 100
0
votes
0
replies
116
views
Molecular Docking, Sars-cov-2
Molecular-docking
updated 20 days ago by
Ram
40k • written 21 days ago by
frogfrapper
• 0
0
votes
0
replies
122
views
Long-reads assembly using Miniasm in NanoGalaxy
assembly
Galaxy
metabarcoding
Nanopore
15 days ago by
Cedrick
• 0
0
votes
3
replies
313
views
Calculating MAF from EAF from a GWAS summary statistics file in R
R
EAF
updated 19 days ago by
Ram
40k • written 22 days ago by
namraahmad173
• 0
0
votes
7
replies
2.7k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr
fold-change
updated 11 days ago by
Ram
40k • written 5.3 years ago by
AP
▴ 80
0
votes
1
reply
177
views
How to generate a consensus sequence from BAM file with bcftools?
bam
bcftools
consensus
updated 14 days ago by
GenoMax
134k • written 14 days ago by
marongiu.luigi
▴ 690
0
votes
1
reply
209
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi
cli
updated 5 days ago by
Ram
40k • written 5 days ago by
O.rka
▴ 680
0
votes
6
replies
247
views
gene correlations in between two groups
gene-expression
correlation
20 hours ago by
biology_inform
▴ 40
0
votes
0
replies
169
views
Current landscape of approaches to scRNA-seq with nanopore sequencers?
scRNA-seq
nanopore
single-cell
2 days ago by
LauferVA
3.7k
0
votes
0
replies
182
views
What metrics to use to calculate variant library evenness or uniformity or bias
library-bias
variant
updated 10 days ago by
Ram
40k • written 11 days ago by
eli_bayat
▴ 90
0
votes
2
replies
398
views
WES CNV analysis
CNV
WES
20 days ago by
Avinash
• 0
0
votes
1
reply
217
views
Significance testing of top vs. random SNPs
SNPs
significance
variance
statistical
updated 5 days ago by
dthorbur
▴ 550 • written 9 days ago by
am29
▴ 30
310 results • Page
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Recent Votes
Comment: How the first sequencing template removed in pair end sequencing
Comment: ncbi error report log for validate fastq issue
Comment: ncbi error report log for validate fastq issue
Comment: module and trait correlation for WGCNA
Peak annotation with HOMER. Statistics with the annStats parameter
Answer: Fetch Fastq files directly for SRA data
Answer: Fetch Fastq files directly for SRA data
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Comment: ncbi error report log for validate fastq issue
by
GenoMax
134k
Can you also provide an example of a GSM ID that fails? I was not aware that you could use GSM ID's directly with `fastq-dump`. I would thi…
Comment: chromosome location
by
biofalconch
▴ 980
If your genome is already in the UCSC genome browser (https://genome.ucsc.edu/), you can visualise the gene structures there, export to a p…
Comment: Saving the output of LD pruning from SNPRelate package as a new GDS file
by
DBScan
▴ 180
You could subset your VCF `C:/Users/HP/Desktop/Magic_FavoritePanel_VCF_SNPs.vcf` to the SNPs you store in `snpset.id` and then create the G…
Comment: ncbi error report log for validate fastq issue
by
1769mkc
★ 1.1k
I will share you the shell script which is part of the pipeline where I basically call the docker image which contains the ncbi-sra tool k…
Comment: Sequence quality drops in the 3' end of the left sequence in paired end. What co
by
GenoMax
134k
This may be one of those things that just happens to be a one-time thing with whatever was going on with this run. Was this sample pooled w…
Comment: ncbi error report log for validate fastq issue
by
GenoMax
134k
Can you provide details of what you are doing and the commands you are using?
Comment: Fetch Fastq files directly for SRA data
by
GenoMax
134k
> fetch fastq files for SRA data hosted by NCBI from AWS data exchange Please provide an example of a SRA accession where you are encount…
Comment: How the first sequencing template removed in pair end sequencing
by
GenoMax
134k
Moving this to an answer since there is a link for a paper. Things could have changed as @rfran010 says but this may be the closest we will…
Comment: Sequence quality drops in the 3' end of the left sequence in paired end. What co
by
Asaf
10k
What machine? (Nextseq? Novaseq?) what library prep method?
Comment: How to determine the total count for each gene in lymphotype B
by
fracarb8
★ 1.2k
If you want the average expression, you should look at `AverageExpression` from seurat which returns the average instead of the sum. `Avera…
Answer: Fetch Fastq files directly for SRA data
by
Umer
▴ 50
You can also use **[Grabseqs][1]**. Easiest way is to use it with anaconda as **conda install -c louiejtaylor grabseqs** But you have…
Answer: chromosome location
by
Umer
▴ 50
What you can do is use **SnapGene** 1. Download the genome (fasta file) 2. Load it into Snapgene 3. Find gene locations based on the …
Comment: Troubles launch IGV on Linux(Debian)
by
barslmn
★ 1.8k
Your log seems fine. Could you add the results of these commands? - Which version of debian are you on? ``` lsb_release -c `…
Comment: How to plot coverage and depth statistics of a bam file
by
jl19
• 0
Hi William, I was trying to use bam2plot you have developed. It was installed on a python evnviroment python version 3.11. The installat…
Comment: Help writing code for a question on my homework
by
Joe
21k
This isn't really the right place for this question. Please ask this as a separate new question, but only if it is bioinformatics related.
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