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760 results • Page
1 of 16
Sort: replies
Rank
Views
Votes
Replies
76
votes
72
replies
20k
views
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 15 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
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 20 days ago by
noodle
▴ 580
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
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
6 days ago by
vytarasov
▴ 180
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 29 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 21 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
946
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
13
votes
14
replies
911
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
1
vote
14
replies
616
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
15 hours ago by
hophuquy0944
• 0
10
votes
14
replies
774
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 10 days ago by
GenoMax
142k • written 16 days ago by
nicole.kavanagh
• 0
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 15 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 7 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
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 27 days ago by
ATpoint
82k • written 28 days ago by
BioinfGuru
★ 1.7k
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 23 days ago by
drstalinantony28
• 0 • written 2.3 years ago by
ymj
▴ 10
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
11
votes
12
replies
1.2k
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 28 days ago by
Ram
43k • written 29 days ago by
iamsmor
• 0
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 8 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 29 days ago by
kjngo
• 0 • written 12.1 years ago by
Gabriel R.
★ 2.9k
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 4 hours ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 18 days ago by
jkbonfield
★ 1.2k • written 4 weeks ago by
me
• 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 21 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
11
replies
645
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
13 hours ago by
egascon
• 0
0
votes
11
replies
535
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
5 days ago by
Tuck898
• 0
4
votes
11
replies
883
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 23 days ago by
LauferVA
4.2k • written 24 days ago by
dominickd
• 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
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 24 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
0
votes
11
replies
714
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
0
votes
10
replies
635
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 17 days ago by
i.sudbery
19k • written 25 days ago by
Patadu94
• 0
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
23 days ago by
DKA
▴ 40
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 29 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 18 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
1
vote
10
replies
889
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
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
0
votes
9
replies
599
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
1 day ago by
Arton
▴ 10
1
vote
9
replies
1.3k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 29 days ago by
Murat
• 0 • written 20 months ago by
Gerard
▴ 10
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
3
votes
9
replies
615
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 23 days ago by
Istvan Albert
100k • written 25 days ago by
Κοσμάς
• 0
4
votes
9
replies
395
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
7 hours ago by
Gabriel R.
★ 2.9k
0
votes
9
replies
600
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 2 days ago by
Wayne
★ 2.0k • written 11 days ago by
JACKY
▴ 140
2
votes
9
replies
695
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 2 days ago by
Pierre Lindenbaum
161k • written 10 days ago by
schmince
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 9 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
1
vote
9
replies
394
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 7 days ago by
i.sudbery
19k • written 10 days ago by
Assa Yeroslaviz
★ 1.8k
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 14 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
1
vote
9
replies
257
views
zero TPM for many gene including housekeeping when using kallisto
RNAseq
4 hours ago by
ashkan
▴ 160
0
votes
9
replies
347
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
1 day ago by
njornet
▴ 20
760 results • Page
1 of 16
Recent Votes
Answer: How to download dbSNP153 vcf files in hg19/GRCH37 version
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
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16k
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Ezequiel
• 0
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alanh
▴ 170
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6.0k
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ashkan
▴ 160
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Umer
▴ 50
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11k
Recent Replies
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool
by
GenoMax
142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
Zhenyu Zhang
★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Details on salmon index
by
Rob
6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
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