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1,000 results • Page
4 of 20
Sort: replies
Rank
Views
Votes
Replies
4
votes
8
replies
1.8k
views
Error while running nf-core/rnaseq pipeline
nf-core
RNA-seq
11 months ago by
eesha28112001
• 0
3
votes
8
replies
625
views
Huge decrease of BUS records using bustools
single-cell
bustools
10X
8 weeks ago by
julien.wollbrett
• 0
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 19 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
1
vote
8
replies
3.9k
views
No gene can be mapped
R
GSEA
updated 4 months ago by
jv
★ 1.8k • written 2.3 years ago by
yang.zhizhang
• 0
1
vote
8
replies
1.1k
views
Mitochondrial genes - TPM calculation bulk RNA-Seq
TPM
RNA-Seq
mtDNA
5 months ago by
nick_b55
▴ 10
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq
deseq2
updated 10 months ago by
Ram
43k • written 3.9 years ago by
kand3e
▴ 60
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 19 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
1
vote
8
replies
2.5k
views
subset data problem
R
seurat
9 months ago by
Andy
▴ 120
2
votes
8
replies
691
views
TCGA Biospecimens Slides Extraction
tcga
updated 9 weeks ago by
Zhenyu Zhang
★ 1.2k • written 10 weeks ago by
jain72744
▴ 10
0
votes
8
replies
335
views
Error in cnetplot enrichplot package
R
updated 6 days ago by
Ram
43k • written 6 days ago by
Farhad
• 0
1
vote
8
replies
1.1k
views
Shannon's Entropy by Sliding Window in R
Sequence
Window
R
Entropy
Sliding
updated 10 months ago by
rohitsatyam102
▴ 850 • written 17 months ago by
Alex
• 0
0
votes
8
replies
653
views
Phobius error: Could not read provided fasta sequence at phobius.pl line 408
Phobius
updated 8 weeks ago by
ido.idobar
▴ 10 • written 3 months ago by
Elizabeth
▴ 30
0
votes
8
replies
9.9k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 10 months ago by
Ram
43k • written 6.8 years ago by
himanimalhotra89
• 0
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 8 months ago by
Ram
43k • written 8.0 years ago by
nikelle.petrillo
▴ 110
2
votes
8
replies
980
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 8 weeks ago by
bharata1803
▴ 560 • written 4 months ago by
LauferVA
4.2k
3
votes
8
replies
988
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST
bowtie2
BWA
alignment
8 months ago by
cheesefish21
▴ 10
5
votes
8
replies
1.9k
views
snpeff install error
snpeff
updated 11 months ago by
Ram
43k • written 12 months ago by
bestone
▴ 30
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
1
vote
8
replies
1.3k
views
Betacoronavirus.00.nsq error
biostars-handbook
corona
updated 10 months ago by
Ram
43k • written 2.3 years ago by
Sam
• 0
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan
SNP
updated 10 months ago by
Ram
43k • written 9.5 years ago by
zhaojianli198322
• 0
0
votes
8
replies
565
views
STAR aligner options
STAR
4 weeks ago by
theophile
• 0
0
votes
8
replies
1.1k
views
BAM header edit with a list of amplicons
samtools
BAM
updated 10 months ago by
Ram
43k • written 2.3 years ago by
ltalignani
• 0
1
vote
8
replies
1.5k
views
counts of cite-seq-count vs. cellrenager varies tremendously
citeseq-count
cellranger
cite-seq
scRNA-seq
updated 4 months ago by
ATpoint
82k • written 9 months ago by
Assa Yeroslaviz
★ 1.8k
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 11 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
4
votes
8
replies
610
views
GCP Snakemake
snakemake
GCP
updated 3 months ago by
Ram
43k • written 3 months ago by
Fadwa
▴ 10
2
votes
8
replies
1.0k
views
VCF file CSQ flag
vcf
exome-sequencing
updated 10 months ago by
Ram
43k • written 10 months ago by
Payal
▴ 160
0
votes
7
replies
1.2k
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 11 months ago by
LauferVA
4.2k • written 11 months ago by
Camilo Andres
▴ 40
3
votes
7
replies
6.4k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 11 months ago by
DareDevil
★ 4.3k • written 6.2 years ago by
win
▴ 970
0
votes
7
replies
1.4k
views
fasterq-dump outputs "Cannot use '--ngc' as ngc file."
snakemake
sra-tools
SRA
updated 10 months ago by
Ram
43k • written 12 months ago by
gernophil
▴ 80
4
votes
7
replies
770
views
Alternative for grep in a for loop
linux
updated 6 months ago by
Ram
43k • written 6 months ago by
Prangan
▴ 20
7
votes
7
replies
591
views
6 follow
PCA plot interpretation (single population)
PCA
GWAS
pruning
12 weeks ago by
Shane
▴ 20
0
votes
7
replies
922
views
Mugsy error -directory must be a directory
Mugsy
updated 7 months ago by
Ram
43k • written 3.4 years ago by
A_heath
▴ 160
3
votes
7
replies
1.4k
views
Find 3'UTRs for species
Assembly
alignment
updated 11 months ago by
Ram
43k • written 4.7 years ago by
Palgrave
▴ 110
0
votes
7
replies
1.1k
views
How to test DEGs from microarray data on RNA-seq dataset
microarray
differential
limma
RNA-seq
expression
prediction
11 months ago by
Llander
• 0
0
votes
7
replies
332
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
GenoMax
141k • written 6 days ago by
Patadu94
• 0
2
votes
7
replies
1.1k
views
error: BLAST database name is missing. Please edit provean.sh file to add the name.
provean
error
updated 8 months ago by
GenoMax
141k • written 8 months ago by
elham
• 0
5
votes
7
replies
837
views
About the value in bigwig file
ATAC-seq
updated 9 months ago by
rfran010
▴ 900 • written 9 months ago by
Chris
▴ 260
0
votes
7
replies
1.6k
views
Comparing the GVF file & VCF file
gvf
dna
vcf
ensembl
ngs
updated 5 months ago by
mickeykuo129
• 0 • written 15 months ago by
Alireza
▴ 30
0
votes
7
replies
457
views
1000 Genome: Cause of duplicate variants with different genotypes
CrossMap
1000Genome
1000G
updated 11 weeks ago by
Giulio Genovese
▴ 390 • written 11 weeks ago by
JourneyToAbyss
▴ 210
3
votes
7
replies
2.6k
views
6 follow
Online BLAST search using R
BLAST
R
updated 10 weeks ago by
SequenceServer
▴ 140 • written 2.7 years ago by
accibio
▴ 20
0
votes
7
replies
408
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 23 days ago by
Papyrus
★ 2.9k • written 24 days ago by
doramora
▴ 10
5
votes
7
replies
958
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
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 19 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
0
votes
7
replies
3.8k
views
MUMmer plot visualization
MUMmer plot
updated 10 weeks ago by
Carlos
• 0 • written 3.2 years ago by
rthapa
▴ 90
0
votes
7
replies
444
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 4 weeks ago by
GenoMax
141k • written 4 weeks ago by
Patadu94
• 0
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly
Trinity
RNA-seq
trimmomatic
updated 10 months ago by
Ram
43k • written 8.1 years ago by
lay_0
▴ 50
3
votes
7
replies
491
views
How does kallisto handle multi mapped reads?
kallisto
updated 9 weeks ago by
dsull
★ 5.9k • written 9 weeks ago by
bioinfo
▴ 150
0
votes
7
replies
1.3k
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
updated 7 months ago by
rfran010
▴ 900 • written 7 months ago by
ccbb7aab4
▴ 20
0
votes
7
replies
952
views
Issue with Merging BCF Files: Invalid INFO id Error
bcftools
updated 5 months ago by
Ram
43k • written 5 months ago by
George
▴ 10
0
votes
7
replies
746
views
Search for specific SNPs in VCF files of patients.
ANNOVAR
vcftools
bcftools
GATK
VCF
updated 4 months ago by
Ram
43k • written 4 months ago by
iarmir
▴ 10
1,000 results • Page
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Comment: NGS forensics: how to know if data is fabricated
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
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Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 540
Working on it - it's actually a bit difficult. Low coverage of ribosomal proteins. Low coverage of housekeeping genes ...I'm trying to find…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 540
I'm a bit against pubpeer - have you ever posted there? My gripe with them is that the posts are heavily moderated and EDITED to the point…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
Thanks Mensur! I'd add that in 9 out of 10 cases, you won't receive a reply to a request for raw data. That's just how scientists are, does…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
I had downloaded the two files in a similar manner actually.
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
ok, i'll try to use fastp. I have only used trimmomatic and cutadapt till now and they dont identify on its own. Except the graph in fastqc…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
Gordon Smyth
★ 7.0k
> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
Comment: PDB related issue
by
noodle
▴ 540
You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
Comment: PDB related issue
by
Mensur Dlakic
★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
If you have Linux the assembly should work on your system, but 8 GB is generally not enough for assembling larger genomes.
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