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1,000 results • Page
4 of 20
Sort: replies
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Votes
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0
votes
8
replies
1.0k
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 11 months ago by
GenoMax
142k • written 11 months ago by
Marta
• 0
5
votes
8
replies
2.0k
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
6
votes
8
replies
1.2k
views
conda: command not found: gatk.
conda
gatk
11 months ago by
bestone
▴ 30
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
3
votes
8
replies
2.0k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 11 months ago by
Ram
43k • written 5.5 years ago by
nagendranp1991
• 0
5
votes
8
replies
2.5k
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
updated 9 months ago by
Jordan M Eizenga
▴ 460 • written 16 months ago by
TN
• 0
1
vote
8
replies
1.2k
views
Shannon's Entropy by Sliding Window in R
Sequence
Window
R
Entropy
Sliding
updated 11 months ago by
rohitsatyam102
▴ 860 • written 18 months ago by
Alex
• 0
0
votes
8
replies
1.6k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools
MarkDuplicates
updated 8 weeks ago by
xiangbinruan
• 0 • written 20 months ago by
Phoebe Magdy
• 0
4
votes
8
replies
1.8k
views
Error while running nf-core/rnaseq pipeline
nf-core
RNA-seq
11 months ago by
eesha28112001
• 0
5
votes
8
replies
1.0k
views
sc-RNA seq pipeline
scRNA-seq
NGS
RNA-Seq
4 months ago by
Researcher
▴ 30
3
votes
8
replies
1.0k
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST
bowtie2
BWA
alignment
9 months ago by
cheesefish21
▴ 10
4
votes
8
replies
1.9k
views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE …
super-enhancers
Enhancers
updated 3 months ago by
jared.andrews07
★ 16k • written 3 months ago by
Manhezz
• 0
0
votes
8
replies
589
views
STAR aligner options
STAR
6 weeks ago by
theophile
• 0
1
vote
8
replies
1.3k
views
Betacoronavirus.00.nsq error
biostars-handbook
corona
updated 11 months ago by
Ram
43k • written 2.3 years ago by
Sam
• 0
4
votes
8
replies
1.2k
views
Error executing nf-core/metaboigniter pipeline
nf-core
metaboigniter
nextflow
updated 8 months ago by
Phil Ewels
★ 1.4k • written 8 months ago by
eesha28112001
• 0
0
votes
8
replies
4.5k
views
Downloading single cell data from NCBI
ncbi
rna-seq
fastq-dump
single-cell
updated 8 months ago by
Ram
43k • written 5.4 years ago by
V
▴ 380
3
votes
8
replies
553
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
7 days ago by
Qroid
▴ 40
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 4 weeks ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
4
votes
8
replies
625
views
GCP Snakemake
snakemake
GCP
updated 3 months ago by
Ram
43k • written 3 months ago by
Fadwa
▴ 10
0
votes
8
replies
1.2k
views
BAM header edit with a list of amplicons
samtools
BAM
updated 11 months ago by
Ram
43k • written 2.3 years ago by
ltalignani
• 0
1
vote
8
replies
2.5k
views
Using NCBIs EDirect to download pubmed abstract
edirect
pubmed
NCBI
updated 10 months ago by
Ram
43k • written 5.9 years ago by
zorn21g
• 0
0
votes
8
replies
437
views
Error in cnetplot enrichplot package
R
updated 21 days ago by
Ram
43k • written 21 days ago by
Farhad
• 0
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 11 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
3
votes
8
replies
935
views
Can these RNAseq runs be combined?
transcriptomics
replicates
RNAseq
updated 10 months ago by
GenoMax
142k • written 10 months ago by
mdrnao
• 0
1
vote
8
replies
519
views
Downsampling fastq file
downsample
fastq
13 days ago by
marco.barr
▴ 100
0
votes
8
replies
1.9k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython
python
updated 11 months ago by
Ram
43k • written 4.5 years ago by
muhammad.khizerkiet
• 0
2
votes
8
replies
719
views
TCGA Biospecimens Slides Extraction
tcga
updated 11 weeks ago by
Zhenyu Zhang
★ 1.2k • written 12 weeks ago by
jain72744
▴ 10
1
vote
8
replies
2.6k
views
subset data problem
R
seurat
9 months ago by
Andy
▴ 120
4
votes
7
replies
618
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 4 weeks ago by
Ram
43k • written 4 weeks ago by
AHerik
▴ 20
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 5 weeks ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
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 6.3 years ago by
win
▴ 980
6
votes
7
replies
1.8k
views
Reference genome for RNA-Seq reads decontamination
FastQ_Screen
RNA-Seq
updated 8 months ago by
Ram
43k • written 4.2 years ago by
gnmcsbnfrmtcsclb
▴ 70
7
votes
7
replies
5.0k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.3 years ago by
stu111538
▴ 80
1
vote
7
replies
844
views
alignment tool for big data
sequence
updated 10 months ago by
Ram
43k • written 4.6 years ago by
gbahramali
▴ 20
5
votes
7
replies
977
views
Salmon index not progressing
salmon
updated 7 months ago by
Michael
54k • written 7 months ago by
camillab.
▴ 160
0
votes
7
replies
2.9k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr
fold-change
updated 8 months ago by
Ram
43k • written 5.9 years ago by
AP
▴ 80
1
vote
7
replies
879
views
Ribosomal cluster
seurat
single-cell
7 months ago by
Chris
▴ 280
2
votes
7
replies
701
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq
contamination
updated 8 weeks ago by
Chris Dean
▴ 410 • written 8 weeks ago by
ev97
▴ 20
1
vote
7
replies
922
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 6 weeks ago by
Ram
43k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
5
votes
7
replies
972
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq
sequencing
updated 11 months ago by
supernovamik
• 0 • written 4.4 years ago by
ee.mohseni.alert
▴ 50
0
votes
7
replies
3.8k
views
MUMmer plot visualization
MUMmer plot
updated 12 weeks ago by
Carlos
• 0 • written 3.2 years ago by
rthapa
▴ 90
4
votes
7
replies
1.5k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome
.bed
haplotypes
HG38
coverage
updated 9 months ago by
GenoMax
142k • written 9 months ago by
LeandroF.
• 0
0
votes
7
replies
659
views
Using Primer3 with python to genotype a SNP at a particular position
primer3
python
position
primer
updated 5 months ago by
Pierre Lindenbaum
161k • written 5 months ago by
Keith
• 0
4
votes
7
replies
2.2k
views
About normalization of the datasets from Harmonized TCGA data
protein
transcript
normalisation
updated 3 months ago by
Ram
43k • written 21 months ago by
qiz218591
▴ 10
3
votes
7
replies
2.2k
views
align_and_estimate_abundance error Trinty
align_and_estimate_abundance
RNA-SEQ
RSEM
Trinity
updated 12 months ago by
Ram
43k • written 2.6 years ago by
Princy
▴ 60
3
votes
7
replies
1.1k
views
Use giraffe in vg
giraffe
vg
updated 10 months ago by
Jordan M Eizenga
▴ 460 • written 10 months ago by
Michal
• 0
0
votes
7
replies
475
views
1000 Genome: Cause of duplicate variants with different genotypes
CrossMap
1000Genome
1000G
updated 3 months ago by
Giulio Genovese
▴ 400 • written 3 months ago by
JourneyToAbyss
▴ 210
2
votes
7
replies
1.8k
views
Technology Stack of NCBI (Genbank, GEO, etc.)
sequence
ncbi
gene
genbank
updated 11 months ago by
Ram
43k • written 6.2 years ago by
navela78
▴ 70
1
vote
7
replies
1.9k
views
for loop in a bash script
bash
updated 10 months ago by
Ram
43k • written 2.6 years ago by
Erika
• 0
1
vote
7
replies
822
views
What could be the rage for Average Coverage after Assembly
viral-genome
spades
coverage
de-novo-assembly
updated 10 months ago by
Ram
43k • written 10 months ago by
mail2steff
▴ 70
1,000 results • Page
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142k
You could use `sarek` (nf-core's exome pipeline) if you don't want to customize or reinvent : https://nf-co.re/sarek/3.4.2
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Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
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Two last seats have just become available. Apply now, if you want them.
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You always need to add the following option when you are using `-p` to count paired-end reads. --countReadPairs If specified, fragm…
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As you stated, your problem is likely division by 0. See this [Cross-Validated][1] post that seems to be very similar to your problem. In …
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Consider using SLURM job arrays if you want to use a `for` loop inside a single SLURM job: https://hpc.nmsu.edu/discovery/slurm/job-arrays/
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the sequence c_000007023807_aloha2_low_cov is duplicated in the reference grep c_000007023807_aloha2_low_cov path/to/reference.fasta
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Thank you so much dthorbur. Yes I am new to imputation analysis. I will follow your kind suggestions. Thanks again!
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I don't know but another way of doing it would be to combine different datasets of different strains that you know are clonal. Then you kno…
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