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1,000 results • Page
2 of 20
Sort: Votes
Rank
Views
Votes
Replies
6
votes
5
replies
700
views
Tests for the linear and non-linear relationship between two genes
ode
drc
correlation
regression
rnaseq
updated 3 months ago by
ATpoint
81k • written 3 months ago by
cwwong13
▴ 40
6
votes
7
replies
553
views
NF-Core ampliseq - Rscript markdown error
nf-core
ampliseq
updated 3 months ago by
Michael
54k • written 3 months ago by
nermze
• 0
6
votes
4
replies
6.5k
views
What is gnomAD allele frequency
AF
gnomAD
updated 3 months ago by
Lhl
▴ 760 • written 3.0 years ago by
Eric Wang
▴ 50
6
votes
3
replies
818
views
trimmomatic and STAR alignments
trimmomatic
STAR
RNAseq
sequencing
reads
updated 11 months ago by
stuart archer
▴ 140 • written 12 months ago by
hamarillo
▴ 70
5
votes
2
replies
904
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 5 months ago by
yhdist
▴ 70 • written 7 months ago by
Cookin
▴ 10
5
votes
8
replies
1.9k
views
snpeff install error
snpeff
updated 11 months ago by
Ram
43k • written 11 months ago by
bestone
▴ 30
5
votes
8
replies
581
views
Multiple threads on ubuntu server
Ubuntu
updated 3 months ago by
colindaven
6.3k • written 3 months ago by
oghzzang
▴ 50
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 9 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 2 days ago by
Ram
43k • written 2.9 years ago by
Mat
▴ 60
5
votes
8
replies
1.0k
views
sc-RNA seq pipeline
scRNA-seq
NGS
RNA-Seq
3 months ago by
subhiksha
▴ 30
5
votes
35
replies
3.6k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 9 months ago by
Jordan M Eizenga
▴ 460 • written 10 months ago by
anivlete
• 0
5
votes
4
replies
1.2k
views
Converting Bam file to Fasta (Zipped)
bedtools
samtools
updated 10 months ago by
Ram
43k • written 18 months ago by
Eliveri
▴ 350
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 9 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
5
votes
1
reply
607
views
Enricher with Gene Symbols
DGE
ClusterProfiler
Enrich
ORA
updated 8 months ago by
bk11
★ 2.3k • written 8 months ago by
Manuel Sokolov Ravasqueira
▴ 100
5
votes
4
replies
664
views
FASTQ to BAM to CRAM to FASTQ
Samtools
5 months ago by
ManuelDB
▴ 80
5
votes
1
reply
674
views
Learning Linux advance commands
grep
awk
linux
sed
updated 6 months ago by
Zhitian Wu
▴ 60 • written 18 months ago by
rheab1230
▴ 140
5
votes
6
replies
1.4k
views
DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
DESeq2
R
RNA-Seq
updated 10 months ago by
Ram
43k • written 4.0 years ago by
Ranan Jyoti Sarma
▴ 90
5
votes
7
replies
923
views
Salmon index not progressing
salmon
updated 6 months ago by
Michael
54k • written 7 months ago by
camillab.
▴ 160
5
votes
3
replies
590
views
Strand bias in supplementary alignments from Nanopore
minimap2
nanopore
strand
updated 5 months ago by
cmdcolin
★ 3.8k • written 5 months ago by
dariober
14k
5
votes
11
replies
986
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 8 months ago by
Ram
43k • written 8 months ago by
Chris
▴ 260
5
votes
7
replies
821
views
About the value in bigwig file
ATAC-seq
updated 9 months ago by
rfran010
▴ 900 • written 9 months ago by
Chris
▴ 260
5
votes
5
replies
1.8k
views
bio-newbie / gene research / tools and methods
methods
research
gene
updated 11 months ago by
Ram
43k • written 6.3 years ago by
wizofe
• 0
5
votes
7
replies
3.1k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP
genome
sequence
updated 6 months ago by
Istvan Albert
100k • written 5.8 years ago by
chris.bird
▴ 10
5
votes
8
replies
1.9k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq
DNA-Seq
contamination
QC
updated 6 months ago by
Jingjingzhang
• 0 • written 3.7 years ago by
from the mountains
▴ 230
5
votes
8
replies
2.4k
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
updated 9 months ago by
Jordan M Eizenga
▴ 460 • written 15 months ago by
TN
• 0
5
votes
3
replies
336
views
samtools view: error reading file
samtools
bowtie2
updated 6 weeks ago by
bioinfo_ga
▴ 70 • written 6 weeks ago by
ray
• 0
5
votes
5
replies
2.4k
views
Quickly retrieve reference genome sequence within python
sequence
python
updated 5 months ago by
Feng Tian
▴ 20 • written 5.6 years ago by
gewa
▴ 20
5
votes
4
replies
1.6k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection
DE-genes
multi-treatments
time-series
updated 10 months ago by
Ram
43k • written 7.7 years ago by
statfa
▴ 760
5
votes
5
replies
546
views
Generate BED file
bed
10 weeks ago by
daffodil
▴ 10
5
votes
1
reply
674
views
Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance
vg
pggb
giraffe
updated 6 months ago by
Jordan M Eizenga
▴ 460 • written 6 months ago by
Kyran
▴ 30
5
votes
10
replies
1.2k
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
7 months ago by
alwayshope
▴ 40
5
votes
7
replies
950
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq
sequencing
updated 11 months ago by
supernovamik
• 0 • written 4.3 years ago by
ee.mohseni.alert
▴ 50
5
votes
10
replies
836
views
Error when viewing a bam file
samtools
updated 10 months ago by
Ram
43k • written 11 months ago by
Chris
▴ 260
5
votes
6
replies
795
views
Calculate the percentage of genomic region covered from the BED file.
NGS
sequencing
genomics
exome
genes
updated 8 months ago by
rfran010
▴ 900 • written 8 months ago by
adarsh_pp
▴ 40
5
votes
3
replies
528
views
Visualisation of accessible regions in single cell atacseq data
visualization
scATAC-seq
single-cell
updated 7 months ago by
Ram
43k • written 7 months ago by
sarahmanderni
▴ 100
5
votes
6
replies
1.7k
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
samtools
bam
bed
updated 10 months ago by
Ram
43k • written 17 months ago by
Eliveri
▴ 350
5
votes
7
replies
1.4k
views
error while using cyvcf2 to parse the vcf file
cyvcf2
vcf
htslib
updated 11 months ago by
Ram
43k • written 23 months ago by
rheab1230
▴ 140
5
votes
5
replies
627
views
Normalization and Genome-Wide Comparisons with Chipseq
chip-seq
Chipseq
Normalization
updated 4 months ago by
Ankit
▴ 500 • written 4 months ago by
zbeddingfield3
▴ 10
5
votes
5
replies
615
views
Counting 705 fasta header characters ('>') in human genome
human-genome
genetics
updated 5 months ago by
ATpoint
81k • written 5 months ago by
10mz1
▴ 10
5
votes
5
replies
505
views
Example MAF Files
MAF
updated 4 months ago by
Ram
43k • written 4 months ago by
anasjamshed
▴ 120
5
votes
3
replies
994
views
abyss-pe genome assembly
konnector
abyss-pe
updated 10 months ago by
Ram
43k • written 5.2 years ago by
Igor Lalin
• 0
5
votes
6
replies
382
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 16 days ago by
Istvan Albert
100k • written 17 days ago by
Pumla
• 0
5
votes
11
replies
1.3k
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 8 months ago by
cmdcolin
★ 3.8k • written 8 months ago by
pablo
▴ 300
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 8 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
5
votes
19
replies
4.0k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 3 months ago by
ATpoint
81k • written 4.9 years ago by
ta_awwad
▴ 340
4
votes
6
replies
2.1k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 9 months ago by
Ram
43k • written 9.0 years ago by
Harish Sanja
▴ 10
4
votes
2
replies
463
views
KEGG DATABASE
DATABASE
KEGG
updated 4 months ago by
jv
★ 1.8k • written 4 months ago by
Sijjil
• 0
4
votes
11
replies
1.7k
views
PCA WITH PLINK
PLINK
updated 8 months ago by
Kevin Blighe
87k • written 8 months ago by
Michelle Guerra
• 0
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter
genome
updated 10 months ago by
Ram
43k • written 4.6 years ago by
Kumar
▴ 120
4
votes
5
replies
2.0k
views
Whole blood single cell RNA-seq dataset?
RNA-Seq
scRNA-Seq
whole blood
single cell
11 months ago by
predeus
★ 1.9k
1,000 results • Page
2 of 20
Recent Votes
Bedtools merge but only if intersection exists
Answer: Korean reference file
Comment: Korean human genome reference file
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
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Recent Awards •
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Popular Question
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yueli7
▴ 250
Popular Question
to
Chirag Parsania
★ 2.0k
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to
LChart
3.9k
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to
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14k
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141k
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Recent Replies
Comment: Korean human genome reference file
by
SeoGyun
• 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you very much
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool
by
GenoMax
141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
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