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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
0
votes
9
replies
480
views
Low number of both surviving reads after trimming
trimmomatic
trimming
28 days ago by
Jay
• 0
3
votes
9
replies
671
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
0
votes
9
replies
580
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
7
votes
9
replies
1.1k
views
Calculation of TMB on gene level
genomics
updated 7 months ago by
svp
▴ 680 • written 7 months ago by
smrutimayipanda
▴ 20
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
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
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
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
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
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
4
votes
9
replies
2.6k
views
Blast+ remote database names
blast
remote
databases
Blastplus
updated 9 months ago by
GenoMax
141k • written 2.3 years ago by
Komalharini
• 0
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
1
vote
9
replies
4.4k
views
Unable to install bioconda and bowtie
bioconda
conda
updated 4 months ago by
rpolicastro
13k • written 19 months ago by
n.anuragsharma
▴ 30
3
votes
9
replies
787
views
Understanding this analysis pipeline
reads
updated 10 months ago by
Ram
43k • written 10 months ago by
artemchuki
• 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
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
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
838
views
Deseq2 error
R
deseq2
6 months ago by
sgadila
• 0
2
votes
9
replies
822
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 2 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
1
vote
9
replies
520
views
miRNA alignment with Bowtie2
bowtie2
6 weeks ago by
Chironex
▴ 40
1
vote
9
replies
658
views
Htseq-count reads with missing mate encountered
htseq
htseq-count
5 months ago by
Bjorn
• 0
4
votes
9
replies
1.2k
views
Snakemake issue with wrappers
Python
Snakemake
5 months ago by
Begonia_pavonina
▴ 150
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
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
4
votes
9
replies
572
views
variant calling
variant-calling
updated 23 days ago by
Ram
43k • written 24 days ago by
dalibenam64
• 0
1
vote
9
replies
619
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
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
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
8
replies
1.3k
views
Creating fastq subsets from existing files
scRNA-seq
umi_tools
cellranger
fastq
8 months ago by
Zack
• 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
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
1
vote
8
replies
969
views
Reads in IGV are mostly in intron regions
Patchseq
RNA-seq
10 months ago by
Kai_Qi
▴ 130
3
votes
8
replies
2.0k
views
Kallisto mapping paired end
Kallisto
mapping
updated 11 months ago by
Ram
43k • written 2.2 years ago by
Dk
▴ 20
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
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
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 9 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
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
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
VCF samtools
vcf
samtools
variant-calling
updated 10 months ago by
Ram
43k • written 2.4 years ago by
Lucía
• 0
0
votes
8
replies
4.4k
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
2
votes
8
replies
2.9k
views
How to convert a database from protein to nucleotide
blastn
unix
blastx
blast
updated 11 months ago by
Ram
43k • written 7.1 years ago by
AJTrunkskun94
• 0
2
votes
8
replies
970
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
0
votes
8
replies
2.4k
views
Cannot process all the reads in a fast5 file?
metagenome
nanopore
basecalling
fastq
6 months ago by
Gio
• 0
0
votes
8
replies
1.0k
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 10 months ago by
GenoMax
141k • written 11 months ago by
Marta
• 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
1
vote
8
replies
1.2k
views
Betacoronavirus.00.nsq error
biostars-handbook
corona
updated 10 months ago by
Ram
43k • written 2.3 years ago by
Sam
• 0
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
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter
genome
updated 10 months ago by
Ram
43k • written 4.6 years ago by
Kumar
▴ 120
0
votes
8
replies
526
views
STAR aligner options
STAR
29 days ago by
theophile
• 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
1,000 results • Page
3 of 20
Recent Votes
Comment: PCA plot
C: RNA seq library size
RNA seq library size
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Convert SAM to BAM
Comment: Should I use unpaired reads from trimmomatic
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Recent Replies
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?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t%d\…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
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