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167 results • Page
1 of 4
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76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
6 days ago by
Kevin Blighe
87k
38
votes
24
replies
1.8k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 1 day ago by
i.sudbery
19k • written 4 days ago by
noodle
▴ 580
8
votes
16
replies
916
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 5 days ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
5
votes
16
replies
647
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
2 days ago by
Ruqaiya
• 0
2
votes
11
replies
875
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 2 days ago by
jkbonfield
★ 1.2k • written 14 days 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 5 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
0
votes
11
replies
547
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
5 days ago by
atowns21
• 0
0
votes
10
replies
473
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
i.sudbery
19k • written 9 days ago by
Patadu94
• 0
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 2 days ago by
cwwong13
▴ 40 • written 6.7 years ago by
lessismore
★ 1.3k
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
2 days ago by
anna
▴ 20
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 2 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
8
replies
401
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 1 day ago by
LauferVA
4.2k • written 3 days ago by
jinyu
▴ 10
1
vote
8
replies
833
views
Adding CB tag to bam file
samtools
bam
updated 6 days ago by
Pierre Lindenbaum
161k • written 13 days ago by
Maria
• 0
1
vote
8
replies
425
views
Downsampling fastq file
downsample
fastq
1 day ago by
marco.barr
▴ 80
8
votes
8
replies
615
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
Aaliya
▴ 10
4
votes
8
replies
624
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 4 days ago by
Alex Reynolds
35k • written 5 days ago by
J
▴ 10
3
votes
7
replies
294
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
2 days ago by
salias
• 0
4
votes
7
replies
556
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
2 days ago by
e.r.zakiev
▴ 200
4
votes
7
replies
482
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 6 days ago by
dsull
★ 5.9k • written 7 days ago by
VITALA
• 0
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 6 days ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
2
votes
7
replies
1.3k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 2 days ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
1
vote
7
replies
466
views
gvcf joint calling
WES
GATK
VCF
gVCF
3 days ago by
zihanss
• 0
1
vote
7
replies
475
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 2 days ago by
bk11
★ 2.4k • written 6 days ago by
starswillfade
▴ 10
4
votes
7
replies
667
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 4 days ago by
dsull
★ 5.9k • written 8 days ago by
qudrat.nii
▴ 10
5
votes
6
replies
431
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 1 day ago by
me
▴ 760 • written 2 days ago by
Mariana
▴ 40
2
votes
6
replies
3.7k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 6 days ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 4 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 1 day ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
10
votes
6
replies
9.9k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 5 days ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
0
votes
6
replies
322
views
Post-imputation plot
michigan-imputation-server
quality-control
just now by
kl
▴ 10
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 2 days ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
0
votes
5
replies
352
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 6 days ago by
GenoMax
141k • written 7 days ago by
Bertalan_Takacs
▴ 90
2
votes
5
replies
438
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
3 days ago by
ashaneev07
▴ 20
0
votes
5
replies
384
views
How should I make kallisto indexes?
kallisto
updated 2 days ago by
dsull
★ 5.9k • written 16 days ago by
bioinfo
▴ 150
0
votes
5
replies
273
views
Telescope issue
Telescope
RNA-seq
updated 5 hours ago by
GenoMax
141k • written 1 day ago by
eleven11
• 0
4
votes
5
replies
265
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 2 days ago by
dsull
★ 5.9k • written 2 days ago by
Kazo
▴ 10
0
votes
5
replies
350
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 4 days ago by
Istvan Albert
100k • written 7 days ago by
sehriban.buyukkilic
▴ 10
2
votes
5
replies
919
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 2 days ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
2
votes
5
replies
329
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
5 days ago by
Lada
▴ 30
2
votes
5
replies
340
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
2 days ago by
analyst
▴ 30
2
votes
4
replies
268
views
from row count to tpm
tpm
row-count
normalization
updated 1 day ago by
Ram
43k • written 9 days ago by
michelafrancesconi9
▴ 20
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 6 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
3
votes
4
replies
341
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
6 days ago by
QX
• 0
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 6 days ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
0
votes
4
replies
228
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 1 day ago by
Ram
43k • written 1 day ago by
Hamtaro
▴ 50
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 2 days ago by
Medhat
9.7k • written 24 months ago by
Vitor1
▴ 120
0
votes
4
replies
224
views
Genbank File Format
gbkformat
1 day ago by
alenew.am
• 0
4
votes
4
replies
429
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 4 days ago by
BioinfGuru
★ 1.7k • written 6 days ago by
Ming Tommy Tang
★ 3.9k
1
vote
4
replies
367
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
2 days ago by
hagl
▴ 10
0
votes
4
replies
218
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
updated 1 day ago by
Michael
54k • written 1 day ago by
Riccardo
▴ 10
167 results • Page
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Comment: What does 'bundle_uuid' refer to in this metadata sheet?
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Comment: Post-imputation plot
by
kl
▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems
by
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82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
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Are those 20% unaligned reads coming after hyper-editing detection?
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I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
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> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
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by
nicole.kavanagh
• 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
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I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
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You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
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Thank you! how would I correct that?
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This is an open science community, not a place to write an email to Michael Love. Please address the entire community.
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