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179 results • Page
2 of 4
Sort: Views
Rank
Views
Votes
Replies
2
votes
3
replies
313
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 3 days ago by
bk11
★ 2.4k • written 8 days ago by
Yoosef
▴ 60
1
vote
4
replies
311
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
2 days ago by
samRayne
• 0
10
votes
3
replies
305
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 5 days ago by
b.contreras.moreira
▴ 180 • written 5 days ago by
ijarne
• 0
0
votes
5
replies
299
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
4 days ago by
me
• 0
0
votes
5
replies
295
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
11 hours ago by
feather-W
• 0
3
votes
4
replies
292
views
Truncated metadata file report from ENA Portal API
ena
python
2 days ago by
Giulia
• 0
0
votes
1
reply
288
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 6 days ago by
andres.firrincieli
3.6k • written 7 days ago by
Antonio
• 0
2
votes
8
replies
288
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Matteo Ungaro
▴ 100
5
votes
5
replies
286
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
5 days ago by
Chris
▴ 280
0
votes
5
replies
284
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
1 hour ago by
SilhouetteQ
• 0
0
votes
1
reply
284
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 3 hours ago by
aw7
▴ 270 • written 23 days ago by
abhishekghadge
• 0
0
votes
2
replies
283
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 15 hours ago by
Zhenyu Zhang
★ 1.2k • written 9 days ago by
yahn
• 0
0
votes
3
replies
282
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
Matthew
• 0
1
vote
2
replies
273
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
batch
ComBat-seq
limma
RNA-seq
removeBatchEffect
6 hours ago by
t.fortunato.asquini
• 0
0
votes
4
replies
271
views
Correlation Analysis
statistics
methylation
NGS
expression
2 days ago by
Researcher
▴ 30
1
vote
1
reply
269
views
Seurat V5 integration
Seurat
integration
updated 4 days ago by
Ram
43k • written 8 days ago by
starswillfade
▴ 10
1
vote
2
replies
260
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 6 days ago by
Weiwen
• 0 • written 7 days ago by
MICOS
▴ 10
0
votes
2
replies
259
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 6 days ago by
Xiaofen
• 0 • written 6 days ago by
toddknutson
▴ 60
0
votes
2
replies
258
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 2 days ago by
GenoMax
142k • written 9 days ago by
Ximena
• 0
0
votes
2
replies
257
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
5 days ago by
sainavyav22
• 0
1
vote
3
replies
256
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 6 days ago by
swbarnes2
14k • written 6 days ago by
Ngrin
• 0
0
votes
2
replies
255
views
How are score_weights calculated in this code?
single-cell
2 days ago by
carolofharvest
▴ 40
4
votes
2
replies
255
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
4 days ago by
mnx0723
• 0
1
vote
3
replies
251
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 2 days ago by
Ram
43k • written 3 days ago by
Omics data mining
▴ 260
0
votes
5
replies
248
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 5 days ago by
Joe
21k • written 5 days ago by
Lemonhope
• 0
0
votes
1
reply
248
views
barcode of TCR-sequencing
barcode
updated 5 days ago by
mizraelson
▴ 60 • written 13 days ago by
yueli7
▴ 250
3
votes
3
replies
246
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
6 days ago by
Adyasha
• 0
0
votes
1
reply
246
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Sony
▴ 10
0
votes
2
replies
242
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
6 days ago by
kalavattam
▴ 190
0
votes
2
replies
242
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 4 days ago by
i.sudbery
19k • written 4 days ago by
Prawesh
• 0
0
votes
2
replies
242
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
6 days ago by
Ahiad Chen Zion
• 0
1
vote
2
replies
238
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 6 days ago by
zx8754
11k • written 7 days ago by
snajafy
• 0
3
votes
3
replies
235
views
what is another word for a BLAST "hit"?
blast
alignment
2 days ago by
dec986
▴ 380
1
vote
3
replies
234
views
STAR aligner error
RNA-seq
STAR
slurm
updated 4 days ago by
Ram
43k • written 5 days ago by
M.
▴ 30
1
vote
3
replies
234
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 3 days ago by
GenoMax
142k • written 4 days ago by
cput
• 0
2
votes
2
replies
226
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 4 days ago by
Michael
54k • written 4 days ago by
ashaneev07
▴ 20
1
vote
3
replies
225
views
Tassel 5 GBS: Is there something wrong with my fastqs?
tassel
fastq
gbs
updated 2 days ago by
GenoMax
142k • written 2 days ago by
meck
• 0
2
votes
2
replies
218
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
55 minutes ago by
Christopher
• 0
0
votes
2
replies
217
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 4 days ago by
Ram
43k • written 5 days ago by
Sumeet
• 0
1
vote
1
reply
217
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 6 days ago by
Michael
54k • written 6 days ago by
Guillermo
• 0
6
votes
2
replies
215
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 3 days ago by
Gordon Smyth
★ 7.1k • written 3 days ago by
gBioStar5
▴ 10
0
votes
2
replies
213
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
3 days ago by
jain72744
▴ 10
0
votes
2
replies
212
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 15 hours ago by
Zhenyu Zhang
★ 1.2k • written 4 days ago by
elisheva
▴ 120
2
votes
3
replies
212
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
3 hours ago by
Azra
▴ 10
0
votes
2
replies
212
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 4 days ago by
swbarnes2
14k • written 6 days ago by
ahmad.sajad4541
• 0
0
votes
2
replies
210
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 2 days ago by
Ram
43k • written 3 days ago by
sainavyav22
• 0
2
votes
3
replies
209
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
ScottDansk
▴ 10
0
votes
1
reply
208
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 2 days ago by
curious
▴ 750 • written 3 days ago by
SeoGyun
• 0
1
vote
1
reply
206
views
Gene ontology and homologs
gene-ontology
updated 6 days ago by
geneontologyhelp
▴ 400 • written 7 days ago by
beshka194
• 0
0
votes
1
reply
203
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Amr
▴ 160
179 results • Page
2 of 4
Recent Votes
Comment: RNA seq analysis
C: What is the best practice of scRNA workflow for multiple patients and samples us
What is the best practice of scRNA workflow for multiple patients and samples using Seurat
Answer: Grouping datasets in Seurat
Grouping datasets in Seurat
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
Answer: Kraken2 database
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Comment: RNA seq analysis
by
Matthias Zepper
4.6k
It is still obscure to me how many different tissues you would like to include into your comparison and what your intended design is. To …
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
You can get a look here https://www.biostars.org/p/9465973/
Answer: Mouse ribosome sequences in fasta format
by
GenoMax
142k
A version of the mouse rDNA repeat can be found here: https://www.ncbi.nlm.nih.gov/nuccore/BK000964 Use the dropdown menu at top-left t…
Comment: Kraken2 database
by
Christopher
• 0
Hello, Mathew. Firstly, thank you for answering my question. **Sorry, what analysis are you trying to perform with these databases?** I a…
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
GenoMax
142k
As long as it is the same GIAB sample you could compare your SNP with the SNP's available for the whole genome set.
Comment: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log
by
yau
• 0
Dear Mensur, Thanks so much for your reply!! In my case, I got 1 control(healthy) and 2 disease mouse Single cell RNA-sew data, so I …
Comment: BWA alignment
by
ATpoint
82k
The relevant code line is precisely the same as in the question.
Answer: imputation through beagle
by
dthorbur
★ 1.9k
Building a reference panel from the samples you intend to impute seems like a very circular approach. Plus, GBS is a reduced representation…
Answer: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log
by
Mensur Dlakic
★ 27k
You seem to have too stringent of a p-value cutoff (1e-5). Hopefully you get the concept of how the interplay of `-log10P-value` and `log2F…
Answer: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log
by
yau
• 0
![enter image description here][1] [1]: /media/images/7199a665-b13a-40c8-a065-313cf2b7
Answer: Using samtools with GCS (google cloud storage) on a docker container seems to gi
by
aw7
▴ 270
This is a bit late, but the first thing to go is to run `samtools --version` and make sure the docker samtools is configured with the the G…
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
by
aw7
▴ 270
I do not think `samtools fixmate` and `markdup` are going to work on PacBio long reads. `fixmate` is for setting and repairing mate inform…
Comment: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
by
Azra
▴ 10
I see, thank you!
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8.5k
From the perspective of a Chinese, I'd like to choose a letter in a famous journal with a high IF. If I'm a PI, I think they are both OK, I…
Comment: Publish a Letter in higher impact vs Research article in lower impact
by
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82k
This is off-topic here. I suggest https://academia.stackexchange.com/ Anyway, since hiring procedures in academia are much focused on IF a…
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