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886 results • Page
1 of 18
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Votes
Replies
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
19 days ago by
Kevin Blighe
88k
10
votes
36
replies
5.9k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA
batch-effect
DESeq2
R
updated 27 days ago by
Ram
43k • written 5.7 years ago by
Kristin Muench
▴ 620
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 11 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
38
votes
24
replies
2.1k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 13 days ago by
i.sudbery
19k • written 16 days ago by
noodle
▴ 580
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 26 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
2 days ago by
vytarasov
▴ 180
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 26 days ago by
Ram
43k • written 5.4 years ago by
iraia.munoa
▴ 130
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 27 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 25 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 27 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 24 days ago by
Hagen
▴ 10 • written 10.3 years ago by
filipzembol
▴ 180
7
votes
16
replies
874
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
14 days ago by
Ruqaiya
• 0
8
votes
16
replies
1.1k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 17 days ago by
bk11
★ 2.4k • written 9 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 6 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 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 10 days ago by
Gordon Smyth
★ 7.1k • written 5 months ago by
raplayer
▴ 10
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 11 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
10
votes
14
replies
695
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 6 days ago by
GenoMax
142k • written 12 days ago by
nicole.kavanagh
• 0
13
votes
14
replies
868
views
High Malat-1 expression in single cell data
single-cell
updated 5 days ago by
t.montserrat.ayuso
▴ 40 • written 14 days ago by
carolofharvest
▴ 40
4
votes
13
replies
995
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 27 days ago by
BioinfGuru
★ 1.7k • written 4 weeks ago by
matteo.levorato
• 0
5
votes
13
replies
1.8k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 23 days ago by
ATpoint
82k • written 24 days ago by
BioinfGuru
★ 1.7k
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 19 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
2
votes
13
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 23 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 3 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
26 days ago by
Ram
43k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 25 days ago by
kjngo
• 0 • written 12.1 years ago by
Gabriel R.
★ 2.9k
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 10 days ago by
rsieber
▴ 10 • written 3.1 years ago by
Kumar
▴ 120
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 25 days ago by
Ram
43k • written 25 days ago by
iamsmor
• 0
30
votes
12
replies
3.9k
views
Trying to understand the maths behind one Limma function
limma
RNA-Seq
batch-effect
updated 28 days ago by
Ram
43k • written 4.0 years ago by
Mozart
▴ 330
9
votes
12
replies
4.2k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 26 days ago by
Ram
43k • written 5.0 years ago by
Mozart
▴ 330
4
votes
12
replies
4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 4 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
3
votes
11
replies
6.0k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 27 days ago by
Ram
43k • written 6.5 years ago by
shania90.lk
▴ 30
2
votes
11
replies
976
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 14 days ago by
jkbonfield
★ 1.2k • written 26 days ago by
me
• 0
1
vote
11
replies
5.5k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 8 days ago by
guanghao
• 0 • written 6.1 years ago by
vivekruhela
▴ 20
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 17 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 20 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
23
votes
11
replies
4.9k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf
fasta
homopolymer
repeat
updated 27 days ago by
Ram
43k • written 5.0 years ago by
WouterDeCoster
47k
0
votes
11
replies
479
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
1 day ago by
Tuck898
• 0
0
votes
11
replies
692
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
18 days ago by
atowns21
• 0
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 26 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
4
votes
11
replies
862
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 20 days ago by
LauferVA
4.2k • written 21 days ago by
dominickd
• 0
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 29 days ago by
Aspire
▴ 330 • written 19 months ago by
Manav
• 0
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 25 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 27 days ago by
Ram
43k • written 7.5 years ago by
linda
• 0
1
vote
10
replies
1.0k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
19 days ago by
DKA
▴ 40
8
votes
10
replies
802
views
bash script
whole-genome-sequencing
updated 28 days ago by
Ram
43k • written 5 weeks ago by
bestone
▴ 30
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 14 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 26 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
7
votes
10
replies
2.8k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 27 days ago by
Ram
43k • written 2.1 years ago by
mmitra
▴ 60
0
votes
10
replies
589
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 13 days ago by
i.sudbery
19k • written 21 days ago by
Patadu94
• 0
1
vote
10
replies
868
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 7 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
886 results • Page
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Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
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Wei-Chen Pan
• 0
Hi, did you solve your problem ? I also encounter same issue but it's `wrapper:"v3.9.0/bio/picard/mergevcfs"`. In my log file, it said:…
Comment: What does the 'E%' represent in BUSCO results?
by
Philipp Bayer
8.5k
No worries! I found the commit with the maths too: https://gitlab.com/ezlab/busco/-/blame/master/src/busco/busco_tools/hmmer.py?page=2#L135…
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Thank you for your answer! It really helped me resolve a doubt!
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8.5k
funny enough i tried the same thing (i've used BUSCO heaps times but never saw the E:! even the manual lists 'C:89.0%[S:85.8%,D:3.2%],F:6.9…
Comment: What does the 'E%' represent in BUSCO results?
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142k
According to ChatGPT: In BUSCO, the "E" category represents "End" or "Endof" gene fragments. These are orthologous groups for which the ge…
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Thank you for the link and details
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GeneC
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Thank you very much for helping with the details.
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thank you :)
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I found the answer when using bcftools. Is there is a way to do this with FilterVcf? bcftools filter --include '(FMT/AD[0:1])/(FMT/A…
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142k
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Hi, here is a breakdown of each part that you asked about: **flag 99**: This indicates various properties of the read alignment. In this c…
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