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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
1
vote
9
replies
520
views
miRNA alignment with Bowtie2
bowtie2
6 weeks ago by
Chironex
▴ 40
1
vote
9
replies
877
views
Command line or python RNA-seq read simulator
simulation
RNA-seq
5 months ago by
i.sudbery
19k
1
vote
9
replies
1.5k
views
blast retrieves "N/A" for taxonomic data
blast
blastn
updated 6 weeks ago by
flavianegrete
• 0 • written 3.4 years ago by
langziv
▴ 50
2
votes
9
replies
825
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 2 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
9
replies
480
views
Low number of both surviving reads after trimming
trimmomatic
trimming
28 days ago by
Jay
• 0
1
vote
9
replies
1.2k
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 10 months ago by
Ram
43k • written 10 months ago by
peavy
• 0
1
vote
9
replies
620
views
Problem with ONT sequencing pipeline. Probably in the Samtools part
bam
samtools
ONT
updated 3 months ago by
GenoMax
141k • written 3 months ago by
Emilio
• 0
3
votes
9
replies
1.7k
views
How to get negative training set if I don't know what constitutes negative?
machine-learning
dna-sequence
blast
updated 5 months ago by
Ram
43k • written 7.6 years ago by
nafizh
• 0
1
vote
9
replies
3.3k
views
build databses for genome using snpEff
annotation
SNP
snpEff
updated 8 months ago by
nehakhilwani18
• 0 • written 5.7 years ago by
StudentBio
• 0
3
votes
9
replies
672
views
STARsolo seg fault without readMapNumber flag
STAR
RNA-seq
STARsolo
Velocyto
updated 6 months ago by
Ram
43k • written 6 months ago by
rbronste
▴ 420
6
votes
9
replies
2.0k
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM
Bowtie
updated 11 months ago by
Ram
43k • written 15 months ago by
luzglongoria
▴ 50
0
votes
9
replies
581
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 14 days ago by
LauferVA
4.2k • written 16 days ago by
Aki
▴ 10
4
votes
9
replies
572
views
variant calling
variant-calling
updated 23 days ago by
Ram
43k • written 24 days ago by
dalibenam64
• 0
0
votes
9
replies
5.4k
views
Calculating FPKM and TPM by hand from htseq-count output?
RNA-Seq
rna-seq
htseq
FPKM
TPM
updated 8 months ago by
ATpoint
82k • written 5.0 years ago by
Joel Wallenius
▴ 210
0
votes
9
replies
979
views
gene id
gene-id
NCBI
updated 10 months ago by
GenoMax
141k • written 10 months ago by
safeassli
• 0
0
votes
9
replies
1.7k
views
WCGNA to Cytoscape
wgcna
cytoscape
rna-seq
updated 11 weeks ago by
Ram
43k • written 3.7 years ago by
ovariohisterectomia
▴ 40
2
votes
9
replies
7.6k
views
6 follow
Read MAP and PED files in PLINK
GWAS
PLINK
updated 4 months ago by
GenoMax
141k • written 6.0 years ago by
ft821525
• 0
2
votes
9
replies
1.2k
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
4 months ago by
ian.will
▴ 30
0
votes
9
replies
1.4k
views
Samtools sam to bam error
samtools
updated 5 months ago by
Andrea
• 0 • written 2.0 years ago by
kb_93
▴ 10
3
votes
9
replies
974
views
Estimate sizes of repeats in a especific Gene
CGG
Fragile-X
11 months ago by
Rafael
▴ 10
0
votes
9
replies
902
views
fragments file generation via Sinto from CellRanger output
scATAC
alignment
scRNA
Sinto
10x
6 months ago by
ntsopoul
▴ 60
1
vote
9
replies
855
views
Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases
python
primers
biopython
updated 6 weeks ago by
Dave Carlson
★ 1.7k • written 6 weeks ago by
Matthew
• 0
0
votes
9
replies
1.5k
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
updated 7 months ago by
rfran010
▴ 900 • written 7 months ago by
pb11
▴ 10
1
vote
9
replies
1.4k
views
Couldn't get a file descriptor referring to the console multiqc
multiqc
updated 11 months ago by
Ram
43k • written 22 months ago by
smithkthedale
▴ 10
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 9 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
0
votes
9
replies
1.1k
views
grep multiple lines form file
shell-script
grep
updated 10 months ago by
Ram
43k • written 3.9 years ago by
harry
▴ 30
1
vote
9
replies
615
views
Approach for multi species comparative transcriptomics and differential expression analyses
DE
RNA-seq
transcriptomics
updated 3 months ago by
dthorbur
★ 1.9k • written 3 months ago by
fish_enthusiast
• 0
4
votes
9
replies
1.0k
views
bcl2fastq troubleshooting all reads dumped to "Undetermined"
demultiplex
illumina
sequencing
updated 4 months ago by
GenoMax
141k • written 4 months ago by
MaxF
▴ 120
1
vote
8
replies
821
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq
deseq2
5 months ago by
pingu77
▴ 20
6
votes
8
replies
1.2k
views
conda: command not found: gatk.
conda
gatk
10 months ago by
bestone
▴ 30
0
votes
8
replies
643
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
1.5k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools
MarkDuplicates
updated 6 weeks ago by
xiangbinruan
• 0 • written 19 months ago by
Phoebe Magdy
• 0
2
votes
8
replies
685
views
TCGA Biospecimens Slides Extraction
tcga
updated 9 weeks ago by
Zhenyu Zhang
★ 1.2k • written 10 weeks ago by
jain72744
▴ 10
1
vote
8
replies
970
views
Reads in IGV are mostly in intron regions
Patchseq
RNA-seq
10 months ago by
Kai_Qi
▴ 130
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
1
vote
8
replies
1.1k
views
How does one access TCGA controlled data in AWS S3?
tcga
aws
updated 6 months ago by
Zhenyu Zhang
★ 1.2k • written 6 months ago by
Cmouli
▴ 10
3
votes
8
replies
981
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
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
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 12 weeks ago by
jared.andrews07
★ 16k • written 3 months ago by
Manhezz
• 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
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
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 17 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
4
votes
8
replies
1.8k
views
Error while running nf-core/rnaseq pipeline
nf-core
RNA-seq
11 months ago by
eesha28112001
• 0
4
votes
8
replies
607
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
3
votes
8
replies
905
views
Can these RNAseq runs be combined?
transcriptomics
replicates
RNAseq
updated 10 months ago by
GenoMax
141k • written 10 months ago by
mdrnao
• 0
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
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
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
1
vote
8
replies
2.4k
views
subset data problem
R
seurat
8 months ago by
Andy
▴ 120
1,000 results • Page
3 of 20
Recent Votes
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Comment: PCA plot
C: RNA seq library size
RNA seq library size
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
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chaco001
▴ 40
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GenoMax
141k
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▴ 140
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BioinfGuru
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Recent Replies
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data
by
bk11
★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
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