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684 results • Page
2 of 14
Sort: Votes
Rank
Views
Votes
Replies
4
votes
1
reply
278
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 21 days ago by
zx8754
11k • written 23 days ago by
Jautis
▴ 570
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 23 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 19 days ago by
chenl
▴ 10 • written 2.6 years ago by
Martyna
• 0
4
votes
6
replies
337
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
3 days ago by
bio_info
▴ 20
4
votes
2
replies
229
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
indexing
salmon
updated 2 days ago by
Rob
6.6k • written 2 days ago by
Tonya S.
▴ 10
4
votes
3
replies
428
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 14 days ago by
Mathew
▴ 150 • written 16 days ago by
Christopher
▴ 10
4
votes
5
replies
501
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
28 days ago by
analyst
▴ 50
4
votes
2
replies
215
views
Duplicated sequence samtools
bowtie2
samtools
updated 14 days ago by
GenoMax
142k • written 14 days ago by
Moinuddin
• 0
4
votes
11
replies
967
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
6 days ago by
J
▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
28 days ago by
anna
▴ 20
4
votes
5
replies
4.5k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 11 days ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
4
votes
1
reply
357
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 12 days ago by
dariober
14k • written 13 days ago by
Holly
▴ 30
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 18 days ago by
Tawny
▴ 180 • written 3.1 years ago by
julia_geh
▴ 20
4
votes
9
replies
675
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 6 days ago by
marco.barr
▴ 130 • written 12 days ago by
diqixiaoyaoer
▴ 20
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 24 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
4
votes
7
replies
466
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
14 days ago by
Chen
• 0
4
votes
7
replies
658
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
28 days ago by
e.r.zakiev
▴ 210
4
votes
6
replies
433
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
4 days ago by
Shicheng Guo
★ 9.4k
4
votes
5
replies
3.5k
views
How to compare compare two Sam files to check mapping
alignment
updated 19 days ago by
DavidStreid
▴ 90 • written 6.5 years ago by
madhu.9124
▴ 60
4
votes
1
reply
375
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
28 days ago by
pairedttest
▴ 10
4
votes
2
replies
303
views
GRCh38.gmap file
gnomix
gmap
23 days ago by
lorena9132
▴ 10
4
votes
3
replies
3.0k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 18 days ago by
Pierre Lindenbaum
162k • written 18 days ago by
Lila M
★ 1.3k
4
votes
0
replies
175
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
28 days ago by
Biostar
2.8k
4
votes
2
replies
309
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
18 days ago by
mnx0723
• 0
4
votes
9
replies
551
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
10 days ago by
Gabriel R.
★ 2.9k
3
votes
3
replies
806
views
Cut&Run and heatmap
and
bowtie2
MACS2
updated 6 hours ago by
sogand
• 0 • written 13 months ago by
qudrat.nii
▴ 10
3
votes
5
replies
447
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
24 days ago by
Maverick
▴ 10
3
votes
2
replies
297
views
imputation through beagle
panel
beagle
reference
imputation
13 days ago by
analyst
▴ 50
3
votes
2
replies
218
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 5 days ago by
GenoMax
142k • written 6 days ago by
ashkan
▴ 160
3
votes
5
replies
486
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
6 days ago by
beantkapoor16
▴ 10
3
votes
2
replies
191
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
5 days ago by
Tuấn Anh
• 0
3
votes
3
replies
473
views
absolute path for symbolic links in Snakefile
Snakemake
updated 18 days ago by
Jesse
▴ 770 • written 5 weeks ago by
yifangt86
▴ 60
3
votes
4
replies
6.3k
views
MAUVE: No gene annotations in Genbank file alignments
software-error
MAUVE
RAST
genbank
alignment
updated 4 days ago by
pramach1
▴ 40 • written 9.8 years ago by
tptacek3050
▴ 70
3
votes
4
replies
454
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 11 days ago by
GenoMax
142k • written 11 days ago by
Pierre Lindenbaum
162k
3
votes
1
reply
236
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 14 days ago by
aw7
▴ 310 • written 18 days ago by
Zeng Hao
▴ 40
3
votes
0
replies
156
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
7 days ago by
Biostar
2.8k
3
votes
8
replies
666
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
21 days ago by
Qroid
▴ 40
3
votes
2
replies
444
views
Extract protein sequence
fasta
alignment
blast
27 days ago by
anna
▴ 20
3
votes
1
reply
228
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 17 days ago by
dthorbur
★ 2.0k • written 18 days ago by
Eren
• 0
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
22 days ago by
Ibrahim Tanyalcin
★ 1.2k
3
votes
7
replies
4.0k
views
Difference in Bismark output methylation call files and coverage files
RRBS
Bismark
DNA-methylation
updated 4 days ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
3
votes
7
replies
452
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
28 days ago by
Sergio A.S.
• 0
3
votes
5
replies
377
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 1 day ago by
Pierre Lindenbaum
162k • written 3 days ago by
QX
• 0
3
votes
8
replies
764
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 21 days ago by
Chris Dean
▴ 410 • written 25 days ago by
sovrappensiero
▴ 100
3
votes
8
replies
6.7k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 25 days ago by
Sd
• 0 • written 5.2 years ago by
Nicolas Rosewick
11k
3
votes
3
replies
315
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 14 days ago by
Ram
44k • written 27 days ago by
Adyasha
• 0
3
votes
4
replies
377
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 10 days ago by
Jeremy Leipzig
22k • written 11 days ago by
Ali
• 0
3
votes
3
replies
339
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 17 days ago by
Ram
44k • written 17 days ago by
Omics data mining
▴ 260
3
votes
6
replies
558
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 15 days ago by
Pine
▴ 20 • written 22 days ago by
snajafy
• 0
3
votes
2
replies
181
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 4 days ago by
ATpoint
82k • written 4 days ago by
egascon
• 0
684 results • Page
2 of 14
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by
Nat.Nataren
▴ 10
I would be contacting the company as a start, and getting access to your raw data.
Comment: txt file to bigwig
by
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82k
Please stop asking questions in existing threads. Delete these two comments and open a new question with all the necessary details to under…
Comment: Venter Genome Vcf
by
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22k
there are some violations in this VCF: - Invalid count number, with fixed count the number should be 1 or higher: key=INFO name=TSA type=St…
Comment: Cut&Run and heatmap
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• 0
Hi all, I am new to cut&run or any peak-related analysis and appreciate any guidance on my issue here: I have analyzed peakcalling .txt …
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Since the locus-tags are unclassified, I used the CDS instead of the locus-tags to retrive their ensembl IDs using ensembl bacteria website…
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Could you find a solution to your problem?
Comment: txt file to bigwig
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sogand
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Hi all, I am new to these kind of analysis and appreciate any guidance on my issue here: I have analyzed peakcalling .txt files that are r…
Answer: Help me with Heatmap
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MolGeek
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Hello! So, what is the correct design ? You will have to ask yourself, what do you want to compare? WT vs mut? If so it will be strain. 2…
Answer: Help me with simple data for RNA seq
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14k
1) you have to say what question you are actually asking. There are few different designs that would address different questions. 2) work…
Comment: identify the coordinate for coding and non_coding region.
by
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mmmm I am not sure. This is how I generate my consnsus sequence # Get consensus fastq file samtools mpileup -uf KT992094.1.fasta…
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GenoMax
142k
Why do you have those N's at the beginning of the sequence? If the remainder of the sequence matches 100% then the initial N's may be wrong…
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6.6k
It's nice that you've gone ahead and done some analysis of these results and their differences on your data yourself. These more general qu…
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In this location there is an "entrez" file which maps ensembl IDs to Entrez. It's probably as definitive as you're going to find: https://…
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Anya
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Tried it just recently with almost the same results. 456 out of 496 IDs for protein-coding genes returned as "NA" even though I can see NCB…
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wget https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt awk -F '\t' '{if($12=="Complete Genome" && $11=…
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