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799 results • Page
1 of 16
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76
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72
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20k
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19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
22 days ago by
Kevin Blighe
88k
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 14 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
87
votes
24
replies
24k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 29 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
38
votes
24
replies
2.2k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 17 days ago by
i.sudbery
19k • written 19 days ago by
noodle
▴ 580
23
votes
23
replies
9.9k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq
removeBatchEffect
batch-effect
edger
updated 29 days ago by
Ram
43k • written 5.4 years ago by
iraia.munoa
▴ 130
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
5 days ago by
vytarasov
▴ 180
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 28 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 20 days ago by
bk11
★ 2.5k • written 10 weeks ago by
Sofia
• 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 10 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 180
7
votes
16
replies
940
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
18 days ago by
Ruqaiya
• 0
34
votes
16
replies
21k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 28 days ago by
Hagen
▴ 10 • written 10.3 years ago by
filipzembol
▴ 180
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 13 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
1
vote
14
replies
597
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
5 hours ago by
hophuquy0944
• 0
13
votes
14
replies
907
views
High Malat-1 expression in single cell data
single-cell
updated 9 days ago by
t.montserrat.ayuso
▴ 40 • written 18 days ago by
carolofharvest
▴ 40
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
1
vote
14
replies
2.5k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 14 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
10
votes
14
replies
766
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 9 days ago by
GenoMax
142k • written 15 days ago by
nicole.kavanagh
• 0
5
votes
13
replies
2.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 26 days ago by
ATpoint
82k • written 27 days ago by
BioinfGuru
★ 1.7k
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 22 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 6 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 28 days ago by
Ram
43k • written 28 days ago by
iamsmor
• 0
16
votes
12
replies
7.5k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 14 days ago by
rsieber
▴ 10 • written 3.2 years ago by
Kumar
▴ 120
9
votes
12
replies
4.2k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 29 days ago by
Ram
43k • written 5.0 years ago by
Mozart
▴ 330
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 28 days ago by
kjngo
• 0 • written 12.1 years ago by
Gabriel R.
★ 2.9k
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 7 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
29 days ago by
Ram
43k
0
votes
11
replies
533
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
4 days ago by
Tuck898
• 0
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 20 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
11
replies
608
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
3 hours ago by
egascon
• 0
2
votes
11
replies
1000
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 18 days ago by
jkbonfield
★ 1.2k • written 29 days ago by
me
• 0
1
vote
11
replies
5.6k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 11 days ago by
guanghao
• 0 • written 6.2 years ago by
vivekruhela
▴ 20
0
votes
11
replies
710
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
21 days ago by
atowns21
• 0
4
votes
11
replies
881
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 23 days ago by
LauferVA
4.2k • written 24 days ago by
dominickd
• 0
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 23 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 29 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 17 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
9
votes
10
replies
7.0k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 28 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
1
vote
10
replies
888
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 11 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
0
votes
10
replies
614
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 17 days ago by
i.sudbery
19k • written 24 days ago by
Patadu94
• 0
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
22 days ago by
DKA
▴ 40
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 13 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
0
votes
9
replies
598
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
1 day ago by
Arton
▴ 10
11
votes
9
replies
7.1k
views
How to choose method to integrate different patient sample together in Seurat
Seurat
scRNA
batch-effect
harmony
updated 29 days ago by
Ram
43k • written 4.3 years ago by
623202215
▴ 80
2
votes
9
replies
938
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 23 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
17 days ago by
anna
▴ 20
3
votes
9
replies
941
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 28 days ago by
Elisabeth Gasteiger
★ 2.4k • written 29 days ago by
Jacky
• 0
3
votes
9
replies
613
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 22 days ago by
Istvan Albert
100k • written 24 days ago by
Κοσμάς
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 8 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
0
votes
9
replies
342
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
1 day ago by
njornet
▴ 20
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by
dvelmeshev
• 0
799 results • Page
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Recent Votes
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
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Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 10
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 10
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index
by
Lorenzo
• 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
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ATpoint
82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
dariober
14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err
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GenoMax
142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input?
by
Pierre Lindenbaum
161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem
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Pierre Lindenbaum
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https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
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DGTool
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I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
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b.contreras.moreira
▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
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