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335 results • Page
2 of 7
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Votes
Replies
0
votes
0
replies
129
views
computeGCBias outputs
GC
bam
deepTools
GCbias
4 days ago by
pablo
▴ 300
0
votes
0
replies
107
views
Pindel zygosity determination
depth
vaf
pindel
Zygosity
4 days ago by
arya.sagittarius
▴ 10
1
vote
3
replies
209
views
How to predict the affinity between Protein and RNA?
Protein-RNAinteractions
prediction
deeplearning
updated 23 hours ago by
dthorbur
★ 1.6k • written 4 days ago by
Alex
• 0
1
vote
1
reply
123
views
Seeking Help with Cell Ranger Multi Error in fixed-RNA-profiling
chromium
fixed-RNA-profiling
cellranger
updated 4 days ago by
Ram
43k • written 4 days ago by
lam
• 0
0
votes
2
replies
172
views
data background noise
noise
data
18 hours ago by
marco.barr
▴ 30
4
votes
6
replies
272
views
Protein loops
protein
Loop
4 days ago by
Curious
▴ 10
0
votes
0
replies
458
views
Looking for guidance on Microbial Association Networks (MANs) Inference with samples from different metagenomics/metatranscriptomics studies
microbialassociationnetworks
metatranscriptomics
metagenomics
netowrkbiology
5 days ago by
sebasar1245
• 0
0
votes
1
reply
111
views
Bed file
bedfile
updated 5 days ago by
Pierre Lindenbaum
160k • written 5 days ago by
Jeet
• 0
0
votes
0
replies
74
views
How can validate hub genes or significant factors using area under the ROC curve (AUC)?
R
AUC
genes
hub
validation
5 days ago by
wyt1995
▴ 30
0
votes
0
replies
83
views
Toxinpred 3.0 tool
peptide
protein
toxin
toxicity
updated 5 days ago by
zx8754
11k • written 5 days ago by
Saurabh
• 0
0
votes
3
replies
216
views
Microarray pbrobe ID to gene ID problem
microarray
updated 4 days ago by
GenoMax
140k • written 5 days ago by
mnx0723
• 0
0
votes
0
replies
92
views
Polysome profiling data
Polysome
updated 4 days ago by
Ram
43k • written 5 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
100
views
What to do with multiple genes in ballgown?
STAR
ballgown
DESeq2
5 days ago by
markusz
▴ 10
1
vote
9
replies
412
views
miRNA alignment with Bowtie2
bowtie2
3 days ago by
Chironex
▴ 40
0
votes
0
replies
83
views
Difference between reading concatenated PE reads into jellyfish and merging paired end .jf outputs independently
Jellyfish
Kmer
GenomeScope
5 days ago by
joshua.j.wright
▴ 10
0
votes
1
reply
132
views
Longitudinal microbiome study - Pooling of data?
longitudinal-microbiome-study
statistics
updated 5 days ago by
Chris Dean
▴ 390 • written 5 days ago by
laura_g
• 0
0
votes
0
replies
95
views
ImmuCellAI
RStudio
ImmuCellAI
updated 5 days ago by
Ram
43k • written 5 days ago by
sana
• 0
0
votes
2
replies
179
views
Is there a program that can predict the sequence of an organisms telomeres just from raw sequencing reads
telomeres
genomics
sequencing
5 days ago by
Mark
• 0
0
votes
1
reply
123
views
Calculating (Groupwise) Log2fold change using values obtained from SST-RMA?
SST-RMA
genes
TAC
thermofisher
foldchange
updated 5 days ago by
ATpoint
81k • written 5 days ago by
purple909
• 0
0
votes
0
replies
96
views
Issue to run gatk4 spark
gatk
spark
5 days ago by
Mojtaba
• 0
2
votes
5
replies
580
views
I am trying to generate a bcf file through samtools mpileup but it taking too long, how long does it usually take to generate a bcf file?
alignment
sam
Bam
samtools
Bioinformatics
updated 5 days ago by
jkbonfield
★ 1.2k • written 6 days ago by
K
• 0
0
votes
1
reply
138
views
SNP and Genes position matching dataframes in R
R
dataframe
updated 6 days ago by
dthorbur
★ 1.6k • written 6 days ago by
QX
• 0
0
votes
1
reply
150
views
Alignment tool of repeat expansion detection
STR
NGS
readexpansion
updated 5 days ago by
Jesse
▴ 740 • written 6 days ago by
adarsh_pp
▴ 40
2
votes
7
replies
499
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq
contamination
updated 5 days ago by
Chris Dean
▴ 390 • written 6 days ago by
ev97
▴ 20
0
votes
0
replies
119
views
HADDOCK 2.4
Protein
Docking
6 days ago by
Preeti
• 0
1
vote
5
replies
233
views
how to convert SummarizedExperiment files to DESeqDataSet??
scRNA-seq
DEG
DESeq2
updated 6 days ago by
Haci
▴ 520 • written 6 days ago by
kayah
• 0
1
vote
3
replies
252
views
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated 6 days ago by
GenoMax
140k • written 7 days ago by
Matt
• 0
0
votes
0
replies
103
views
SAMstat mapping quality report MAPQ gt vs MAPQ lt
Sequencing
mapping
samstat
7 days ago by
njornet
▴ 10
3
votes
3
replies
380
views
I can't add VAF from population for all of my variants from VCF file
genomics
vcf
gnomad
updated 6 days ago by
Ram
43k • written 8 days ago by
Samuel
▴ 20
1
vote
4
replies
246
views
Some questions about bulk RNA-seq data normalization
RNA-seq
NGS
bulk
normalize
7 days ago by
feather-W
• 0
2
votes
4
replies
237
views
repeatseq compilation issues
NGS
Repeats
repeatseq
repeatexpansion
Genomics
updated 7 days ago by
Michael
54k • written 7 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
104
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
7 days ago by
CTLong
▴ 90
0
votes
0
replies
93
views
compare the assembler MaSuRCA and SPAdes for assembly unmapped reads
SPAdes
unmapped_reads.
assembly.
MaSuRCA.
7 days ago by
Sony
▴ 10
0
votes
0
replies
111
views
MG-RAST KEGG KO Search
mg-rast
kegg
metagenomics
ko
7 days ago by
Jeremy
▴ 880
0
votes
5
replies
342
views
Same NCBI IDs for different Ensembl IDs / Multiple NCBI IDs for an Ensembl ID
KEGG
ENTREZ
ENSEMBL
6 days ago by
Maxwell
• 0
1
vote
9
replies
763
views
Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases
python
primers
biopython
updated 6 days ago by
Dave Carlson
★ 1.6k • written 7 days ago by
Matthew
• 0
0
votes
1
reply
136
views
Snakemake wrapper issue
fastqc
snakemake
updated 7 days ago by
Ram
43k • written 7 days ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
93
views
MIRA runs yielding different assemblies with same input data and parameters
MIRA
replication
denovo
assembly
7 days ago by
btc347
• 0
0
votes
1
reply
138
views
Understanding Uncommon Genotype Formats in VCF Files Generated by nf-core RNAvar Pipeline
genotype
rnaseq
updated 7 days ago by
Pierre Lindenbaum
160k • written 7 days ago by
ASid
▴ 40
2
votes
2
replies
183
views
ggplot2 installation
ggplot2
updated 7 days ago by
rpolicastro
13k • written 7 days ago by
safeassli
• 0
0
votes
1
reply
138
views
How to perform enrichment p-value for a motif
Enrichment
statistics
updated 7 days ago by
Trivas
★ 1.7k • written 7 days ago by
Apex92
▴ 280
0
votes
3
replies
740
views
Corset error reading input files
corset
updated 7 days ago by
Ram
43k • written 2.3 years ago by
scarey
• 0
1
vote
5
replies
244
views
Merging bam files from different runs
samtools
bam
updated 7 days ago by
GenoMax
140k • written 7 days ago by
shpak.max
▴ 40
0
votes
0
replies
87
views
Signac LinkPeaks warning about feature.weights
R
signac
linkpeaks
7 days ago by
asap_student
• 0
0
votes
0
replies
86
views
edgeR paired analysis with three conditions
edgeR
7 days ago by
suraj
• 0
0
votes
5
replies
269
views
Bedtools getfasta: error
getfasta
bedtools
updated 7 days ago by
GenoMax
140k • written 8 days ago by
ummeswaiba
• 0
0
votes
2
replies
162
views
RNA-seq DE with AAV injection
AAV
RNA-seq
edgeR
enrichment
updated 7 days ago by
rpolicastro
13k • written 7 days ago by
CriticalP
• 0
0
votes
0
replies
87
views
DMRcate for sequencing data
DMRcate
DNA-methylation
differential-methylation
updated 7 days ago by
Ram
43k • written 8 days ago by
alejandrarodrigu21
• 0
0
votes
0
replies
90
views
How can I conduct a meta-analysis of RNA-seq or microarray data?
R
RNA-seq
microarray
meta-analysis
8 days ago by
wyt1995
▴ 30
2
votes
1
reply
134
views
Computing the neighborhood graph in single cell pipeline
single-cell
knn
updated 8 days ago by
ATpoint
81k • written 8 days ago by
QX
• 0
335 results • Page
2 of 7
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Comment: BAM to CRAM and BAM recover with smaller size
Comment: Average expression of a sample in single-cell data
A: Normalize FPKM values for cross-sample comparisons?
Answer: ColabFold
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Troubleshooting a REGENIE sex-stratified GWAS
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Answer: Ribo and RNA seq analysis
by
Manu Ayllon
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I got it making use of blastn, creating first a database with the RNA sequences and doing blast with the Ribo-seq sequences as query. The p…
Comment: Deeptools scale issue for plotHeatmap
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Learner
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Hi Devon, Thanks a lot for the reply. DNA methylation file has 19466838 lines while domains has 92409 lines.
Answer: why there is an asterisk symbol at the end of each proteins sequences offasta fi
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Juke34
8.5k
It corresponds to stop codon but in theory GTF format does not have stop codon in CDS. Keep in mind that it exists stop codon reading th…
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That is an entirely different analysis and depends on the testing Framework. If you use the commonly-used Wilcox test or something like lim…
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@dodausp Did you ever find a reason for this? I am having the same problem
Comment: Troubleshooting a REGENIE sex-stratified GWAS
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Sex chromosomes are always a bit tricky to handle in associations studies. How many male cases and male controls you have for this phenoty…
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And I also change the chrom name in the .sizes file. That works perfect. Thank you very much!
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Thanks for the response! I also was wondering to ask if you have found the log-norm also working fine in terms of downstream analysis like …
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Great solutions on this page, the old web page has been replace with new one, so you need to use the new link, and it will work: old lin…
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unless your cram in sorted on query rather than on coordinate, your cram must be first sort processed with collate: https://twitter.com/lh…
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Well, I guess expression could be measured from the DNA indirectly such as with RNA Pol II binding to DNA via ChIP-seq but then the OP shou…
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