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186 results • Page
2 of 4
Sort: Views
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Views
Votes
Replies
1
vote
2
replies
311
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
4 days ago by
M.
▴ 30
0
votes
1
reply
304
views
Snakemake fails to find conda in PBS
snakemake
updated 1 day ago by
tim.booth
▴ 60 • written 28 days ago by
yixinzeng
• 0
0
votes
1
reply
301
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 5 days ago by
aaron.stevens
• 0 • written 3 months ago by
sativus
▴ 20
1
vote
3
replies
300
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 1 day ago by
bk11
★ 2.4k • written 6 days ago by
Yoosef
▴ 60
10
votes
3
replies
296
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 2 days ago by
b.contreras.moreira
▴ 180 • written 3 days ago by
ijarne
• 0
1
vote
3
replies
296
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
5 days ago by
Dora
▴ 10
0
votes
10
replies
295
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
updated 10 hours ago by
swbarnes2
14k • written 16 hours ago by
Tuck898
• 0
1
vote
3
replies
295
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
5 days ago by
Lada
▴ 30
2
votes
5
replies
291
views
Importing a fastq file
Fastq
updated 1 day ago by
size_t
▴ 120 • written 2 days ago by
oumo
• 0
0
votes
1
reply
284
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 3 days ago by
andres.firrincieli
3.6k • written 4 days ago by
Antonio
• 0
0
votes
5
replies
277
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
2 days ago by
me
• 0
5
votes
5
replies
274
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
3 days ago by
Chris
▴ 280
1
vote
4
replies
272
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
12 hours ago by
rackbersingh
• 0
0
votes
2
replies
270
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 4 days ago by
GenoMax
142k • written 5 days ago by
mropri
▴ 150
0
votes
1
reply
263
views
creating batch colum for batch correction
batch-correction
combat
4 days ago by
Expert
▴ 10
4
votes
2
replies
263
views
GRCh38.gmap file
gnomix
gmap
6 days ago by
lorena9132
▴ 10
0
votes
2
replies
256
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
3 days ago by
sainavyav22
• 0
1
vote
2
replies
256
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 3 days ago by
Weiwen
• 0 • written 4 days ago by
MICOS
▴ 10
1
vote
1
reply
256
views
Seurat V5 integration
Seurat
integration
updated 2 days ago by
Ram
43k • written 5 days ago by
starswillfade
▴ 10
0
votes
2
replies
249
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 14 hours ago by
GenoMax
142k • written 7 days ago by
Ximena
• 0
4
votes
2
replies
247
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
2 days ago by
mnx0723
• 0
4
votes
2
replies
246
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 6 days ago by
Ram
43k • written 7 days ago by
carolofharvest
▴ 40
1
vote
2
replies
245
views
Downloading full alignments from Pfam
pfam
5 days ago by
bef1
• 0
0
votes
1
reply
245
views
barcode of TCR-sequencing
barcode
updated 3 days ago by
mizraelson
▴ 60 • written 10 days ago by
yueli7
▴ 250
4
votes
1
reply
242
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 5 days ago by
zx8754
11k • written 6 days ago by
Jautis
▴ 560
0
votes
1
reply
241
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Sony
▴ 10
0
votes
2
replies
241
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 4 days ago by
Xiaofen
• 0 • written 4 days ago by
toddknutson
▴ 60
3
votes
3
replies
239
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
4 days ago by
Adyasha
• 0
0
votes
3
replies
239
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 1 day ago by
Pierre Lindenbaum
161k • written 2 days ago by
Matthew
• 0
2
votes
2
replies
239
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB
protein
STRING-DB-API
5 days ago by
brandon
• 0
0
votes
2
replies
238
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
4 days ago by
kalavattam
▴ 190
0
votes
3
replies
238
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 4 days ago by
swbarnes2
14k • written 4 days ago by
Ngrin
• 0
0
votes
2
replies
237
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
3 days ago by
Ahiad Chen Zion
• 0
3
votes
4
replies
234
views
Truncated metadata file report from ENA Portal API
ena
python
13 hours ago by
Giulia
• 0
0
votes
2
replies
231
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 1 day ago by
i.sudbery
19k • written 2 days ago by
Prawesh
• 0
0
votes
5
replies
228
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 2 days ago by
Joe
21k • written 3 days ago by
Lemonhope
• 0
1
vote
2
replies
228
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 4 days ago by
zx8754
11k • written 4 days ago by
snajafy
• 0
0
votes
1
reply
226
views
Help with DGEList function
DGEList
R
updated 5 days ago by
marco.barr
▴ 100 • written 6 days ago by
Natali
• 0
1
vote
3
replies
222
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 1 day ago by
GenoMax
142k • written 2 days ago by
cput
• 0
0
votes
3
replies
220
views
STAR aligner error
RNA-seq
STAR
slurm
updated 2 days ago by
Ram
43k • written 3 days ago by
M.
▴ 30
0
votes
1
reply
217
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 6 days ago by
Ram
43k • written 7 days ago by
Rob
▴ 170
0
votes
4
replies
216
views
Correlation Analysis
statistics
methylation
NGS
expression
1 hour ago by
Researcher
▴ 30
1
vote
1
reply
212
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 3 days ago by
Michael
54k • written 4 days ago by
Guillermo
• 0
0
votes
2
replies
210
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 2 days ago by
Ram
43k • written 3 days ago by
Sumeet
• 0
0
votes
2
replies
208
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 2 days ago by
swbarnes2
14k • written 3 days ago by
ahmad.sajad4541
• 0
1
vote
1
reply
205
views
Gene ontology and homologs
gene-ontology
updated 4 days ago by
geneontologyhelp
▴ 400 • written 5 days ago by
beshka194
• 0
1
vote
2
replies
200
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 1 day ago by
Michael
54k • written 2 days ago by
ashaneev07
▴ 20
2
votes
3
replies
195
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
ScottDansk
▴ 10
1
vote
1
reply
194
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 6 days ago by
Ram
43k • written 7 days ago by
adi.gershon1
• 0
0
votes
2
replies
194
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
2 days ago by
Nicholas
• 0
186 results • Page
2 of 4
Recent Votes
Answer: Tissue-specific DEG analysis with DEseq2
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
Answer: what is another word for a BLAST "hit"?
Comment: what is another word for a BLAST "hit"?
Comment: what is another word for a BLAST "hit"?
Comment: How can I merge GFF files together to produce a file with gene functions from bo
Comment: Contig assembly task, errors
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Comment: Correlation Analysis
by
Researcher
▴ 30
Thank you so much. I ran based on the above code and found that all gene columns have the same values, which you obtain as the average corr…
Answer: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
use bcftools merge with --force-samples and then use jvarkit https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ to replace the no-call …
Answer: In IGV is this a heterogeneous mutation or false call?
by
swbarnes2
14k
Since all the reads that show the alternate allele have to be clipped to align there, I'd say those reads are misaligned. I would say that…
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
GenoMax
142k
> Here's a few lines from the head of the raw fastq If your files are actually compressed (as their names suggest) then you should not be …
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
GenoMax
142k
If you added the `\` before the `+` then there is no need for it. It makes it appear that the sequences are not in proper fastq format. Ple…
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
Mensur Dlakic
★ 27k
This seems to be the same unanswered question as before, except that its description is split over two threads. You are now forcing us to r…
Answer: what is another word for a BLAST "hit"?
by
dec986
▴ 380
I'll probably go with "matches" even though it doesn't sound as good as just "hit"
Comment: what is another word for a BLAST "hit"?
by
bk11
★ 2.4k
> hits from BLAST hits sequences
Comment: what is another word for a BLAST "hit"?
by
Pierre Lindenbaum
161k
> is there a synonym for hits from BLAST? alignment
Comment: How are score_weights calculated in this code?
by
Ram
43k
Is this ALL the context you can give us?
Comment: Genome Assembly task + Protein Translation, assignment advice on a question
by
Ram
43k
Where did you copy-paste this from? It looks like an assignment question.
Comment: Contig assembly task, errors
by
rackbersingh
• 0
Hi Phillip, Thanks for sharing you knowledge and funnily enough this really was an amplitude test, but anyways your sharing of knowledge h…
Comment: Can I readmap short reads to rDNA references?
by
GenoMax
142k
If these are short reads and the organisms are related then you are going to have a difficult time classifying the reads.
Comment: extract viral protein of interest from 10k whole viral genomes
by
GenoMax
142k
With a large dataset it is always best to do the search locally (or in the cloud, if you don't have necessary hardware available locally).
Comment: Truncated metadata file report from ENA Portal API
by
Giulia
• 0
Thank you so much for your hint! I'll look into this!
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