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135 results • Page
2 of 3
Sort: replies
Rank
Views
Votes
Replies
1
vote
2
replies
235
views
highlight regions in a dot-plot?
figure
dotplot
alignment
synteny
5 days ago by
Buffo
★ 2.2k
0
votes
2
replies
267
views
Import or read Snapgene .dna files into R
R
.dna
snapgene
4 days ago by
eggrandio
▴ 40
1
vote
2
replies
248
views
DEgs RNAseq
RNAseq
2 days ago by
Juan
• 0
0
votes
2
replies
1.7k
views
Fourfold degenerate codons in VCF File
vcf
genome
updated 4 days ago by
Ram
39k • written 4.4 years ago by
crippa.to
• 0
1
vote
2
replies
144
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
4 hours ago by
Pegasus
▴ 90
0
votes
2
replies
220
views
Error in download library file in expression console software
expression
microarray
console
6 hours ago by
Mohammad
• 0
0
votes
2
replies
149
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
1 day ago by
pg45863
• 0
0
votes
2
replies
189
views
Repbase database and transposon sequence
TE
TSD
TIRs
Tpase
4 days ago by
manaswiniparija3
▴ 10
0
votes
1
reply
847
views
Get publication counts per gene per year
eutilities
updated 4 hours ago by
Ram
39k • written 4.2 years ago by
abhijit.synl
▴ 60
0
votes
1
reply
244
views
too many zeros in 16S rRNA amplicon sequencing data
16S
rRNA
updated 3 days ago by
andres.firrincieli
3.3k • written 4 days ago by
zhangdengwei
▴ 180
1
vote
1
reply
2.6k
views
Comparing time series expression data
time-series
gene-expression
updated 5 hours ago by
Ram
39k • written 5.8 years ago by
The
▴ 180
0
votes
1
reply
192
views
Identifying Mutation Frequency Changes in MSAs over time?
Mutation
Fasta
MSA
MutationRate
RNA-Seq
updated 4 days ago by
Vincent Laufer
★ 2.8k • written 5 days ago by
Saran
▴ 20
0
votes
1
reply
56
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 4 hours ago by
andres.firrincieli
3.3k • written 4 hours ago by
kamanovae
▴ 80
0
votes
1
reply
140
views
making metadata file for differential gene expression analysis
RNAseq
updated 5 days ago by
Basti
★ 1.5k • written 5 days ago by
Sara
▴ 220
0
votes
1
reply
64
views
sorting BAM file
BAM
updated 5 hours ago by
Ram
39k • written 7 hours ago by
Mohammad Amin
• 0
0
votes
1
reply
230
views
problem of Global Biobank Meta-analysis Initiative
GWAS
updated 2 days ago by
Fabio Marroni
★ 3.0k • written 3 days ago by
1362321710
• 0
1
vote
1
reply
162
views
Import Pymol into Python Script
Pymol
python
updated 5 days ago by
Wayne
★ 1.8k • written 5 days ago by
jdrohan
• 0
0
votes
1
reply
121
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
updated 2 hours ago by
Jesse
▴ 540 • written 1 day ago by
J.F.Jiang
▴ 900
0
votes
1
reply
199
views
Finding Kinetic Parameters from Western Blot images
image-processing
western-blot
updated 4 days ago by
Ram
39k • written 4 days ago by
Vijeth
• 0
0
votes
1
reply
695
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure
pymol
protein
pdb
python
updated 5 hours ago by
Joe
21k • written 4 days ago by
Aatif Hashmi
• 0
0
votes
1
reply
54
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 2 hours ago by
GenoMax
129k • written 5 hours ago by
fafad046
• 0
0
votes
1
reply
932
views
Questions about assembly of large metagenomics dataset
assembly
metagenomics
megahit
updated 5 days ago by
Ram
39k • written 4.5 years ago by
zorrilla
• 0
0
votes
1
reply
62
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
updated 6 hours ago by
GenoMax
129k • written 6 hours ago by
Mohd
• 0
1
vote
1
reply
985
views
cfDNA target seq vs. cfDNA WES
cfDNA
updated 6 days ago by
Ram
39k • written 4.9 years ago by
genetic
▴ 40
0
votes
1
reply
220
views
Variant Annotation
Variant-Annotation
VCF
R
updated 4 days ago by
Ram
39k • written 4 days ago by
Chethana
• 0
0
votes
1
reply
151
views
Samtools index and sambamba-depth error?
linux
samtools
indexing
sambamba
updated 6 days ago by
Pierre Lindenbaum
154k • written 6 days ago by
MobiusT
▴ 10
0
votes
1
reply
105
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 6 hours ago by
Ram
39k • written 16 hours ago by
chengc2016zzu
• 0
0
votes
1
reply
800
views
Segmentation method in CNV
CNV
sequencing
updated 1 hour ago by
Ram
39k • written 4.1 years ago by
nesma.abdelaziz
• 0
0
votes
1
reply
137
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated just now by
Ram
39k • written 1 day ago by
barrypraveen
▴ 110
0
votes
1
reply
162
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 12 hours ago by
fracarb8
▴ 950 • written 1 day ago by
Sun
• 0
1
vote
1
reply
216
views
DownsampleSam
picard
DownsampleSam
updated 3 days ago by
Pierre Lindenbaum
154k • written 3 days ago by
mathalfilip
• 0
0
votes
1
reply
182
views
How to find marker genes for whole tissue from several different sub-tissue scRNAseq datasets
prediction
marker
scRNAseq
updated 6 days ago by
jv
★ 1.2k • written 7 days ago by
nickeener
▴ 50
0
votes
1
reply
164
views
Why coordinate sort is required in sambamba depths?
sorting
coordinate
sambamba
linux
samtools
updated 1 day ago by
Pierre Lindenbaum
154k • written 1 day ago by
MobiusT
▴ 10
0
votes
1
reply
750
views
Where can I find Time Series Multi-Omics human cancer datasets
multi-omics
cancer
time-series
updated 7 hours ago by
Ram
39k • written 3.2 years ago by
donnieDarko
• 0
0
votes
1
reply
131
views
ABySS Process Killed
ABySS
genome
assembly
updated 1 day ago by
GenoMax
129k • written 1 day ago by
asarcillo
• 0
0
votes
1
reply
296
views
Deferentially expressed gene with high log2foldchange by DESeq2; but not meaningful at the individual level
DESeq2
RNA-seq
DGEA
updated 4 days ago by
Vincent Laufer
★ 2.8k • written 4 days ago by
Sara
▴ 10
0
votes
1
reply
219
views
Error while running Megahit
Megahit
updated 2 days ago by
Mensur Dlakic
★ 23k • written 3 days ago by
abhiramiabhirami9072
• 0
1
vote
1
reply
1.3k
views
Can HISAT2 be invoked in bash shell, and can it be fed variables or names with wildcards as inputs?
Bash
Shell
HISAT2
updated 4 days ago by
Ram
39k • written 4.3 years ago by
RNAseqer
▴ 240
0
votes
0
replies
1.7k
views
Artificial Neural Networks applied to environmental data
artificial-neural-networks
time-series
ANN
updated 5 hours ago by
Ram
39k • written 8.5 years ago by
felipehcoutinho
▴ 10
0
votes
0
replies
89
views
Merging multiple PLINK files
plink
merging
1 day ago by
Nejla
• 0
0
votes
0
replies
675
views
Brownian motion : Understanding the output of mvBM function.?
Phylogeny
Brownian
updated 5 days ago by
Ram
39k • written 4.5 years ago by
naveen_gabriel
• 0
1
vote
0
replies
442
views
Using STAR SJ.out.tab file to identify novel ncRNAs
time-course
RNA-seq
ncRNA
STAR
updated 7 hours ago by
Ram
39k • written 17 months ago by
jennifer.conrad84
▴ 10
0
votes
0
replies
450
views
Normalizing multiple conditons all together
RMA
microarray
time-series
updated 7 hours ago by
Ram
39k • written 2.6 years ago by
Raheleh
▴ 250
0
votes
0
replies
159
views
Chipseq data peak calling issue
ChIP-seq
RNA
sequencing
updated 2 hours ago by
Ram
39k • written 4 days ago by
Adyasha
• 0
0
votes
0
replies
159
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
updated 2 hours ago by
Ram
39k • written 2 days ago by
Vincent Laufer
★ 2.8k
0
votes
0
replies
58
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase
Databases
enzymes
Restriction
17 hours ago by
Mahmoud Reda
▴ 10
0
votes
0
replies
43
views
Converting rds file to h5ad and saving raw counts as X
R
seurat
updated 10 hours ago by
zx8754
11k • written 10 hours ago by
sidrah.maryam
▴ 50
0
votes
0
replies
835
views
Time series analysis for RNA-seq paired samples
TimeSeriesExperiment
RNA-Seq
time-series
updated 5 hours ago by
Ram
39k • written 3.3 years ago by
essief
• 0
0
votes
0
replies
110
views
Allowed Deviations in fixed bond length and bond angles in peptides from the typical values.
protein
bondangles
structure
fragbuilder
python
6 days ago by
physicsvigna
• 0
0
votes
0
replies
989
views
FRMA processing on two different datasets of affy u133A not same dimensions
u133A
R
frma
affy
updated 3 days ago by
Ram
39k • written 4.2 years ago by
jmannhei
▴ 10
135 results • Page
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Recent Votes
Comment: Regular Expression for conversion
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
A: PolyPhen Humdiv vs HumVar discrepancies
A: How To Get Annotation For Bed File From Another Bed File
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Comment: How to make a dotplot for bulk RNA average expression ?
by
bhumm
▴ 40
I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
Answer: What is the best way to clean bulk RNA-seq data?
by
swbarnes2
13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Vincent Laufer
★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file
by
bhumm
▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline
by
ATpoint
72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline
by
swbarnes2
13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline
by
Ram
39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline
by
Ram
39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree
by
GenoMax
129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline
by
Ram
39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index
by
ashleymb1116
• 0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index
by
GenoMax
129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
Comment: Salmon Index
by
ashleymb1116
• 0
Thank you, yes I am using the newer version of Ensembl. Above with Arabidopsis is the example Salmon gave, I am using the Bos Taurus files.…
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