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1,000 results • Page
4 of 20
Sort: Votes
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Views
Votes
Replies
4
votes
5
replies
1.4k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 11 months ago by
Ram
43k • written 6.8 years ago by
CY
▴ 750
4
votes
9
replies
1.2k
views
Snakemake issue with wrappers
Python
Snakemake
5 months ago by
Begonia_pavonina
▴ 150
4
votes
11
replies
1.8k
views
PCA WITH PLINK
PLINK
updated 8 months ago by
Kevin Blighe
87k • written 8 months ago by
Michelle Guerra
• 0
4
votes
7
replies
995
views
Statistical test to compare data across timepoints
Statistics
updated 6 months ago by
Matthias Zepper
4.5k • written 6 months ago by
Sean
▴ 20
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
4
votes
7
replies
540
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 11 days ago by
Ram
43k • written 12 days ago by
AHerik
▴ 20
4
votes
5
replies
533
views
Which refseq_protein db to choose for zingiberaceae
local
blastp
blast
updated 8 months ago by
GenoMax
141k • written 8 months ago by
Nilo
• 0
4
votes
3
replies
307
views
Getting less DE genes when incorporating all samples
RNA-seq
differential-expression
deseq2
updated 9 weeks ago by
jv
★ 1.8k • written 10 weeks ago by
shome
▴ 10
4
votes
4
replies
3.3k
views
Unable to install Autogrid4
autogrid
software-error
autogrid4
updated 11 months ago by
Ram
43k • written 3.1 years ago by
roybatty269
• 0
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
4
votes
5
replies
2.0k
views
Whole blood single cell RNA-seq dataset?
RNA-Seq
scRNA-Seq
whole blood
single cell
12 months ago by
predeus
★ 1.9k
4
votes
3
replies
390
views
Single cell analysis of Cancer
cancer
single-cell
RNA-seq
updated 10 weeks ago by
GenoMax
141k • written 10 weeks ago by
moustafa_abohawya
▴ 20
4
votes
6
replies
1.8k
views
Failure in installing the ggtree, enrichplot, and ggtree (Bioconductor packages )
Bioconductor
updated 9 months ago by
GenoMax
141k • written 9 months ago by
applepie
• 0
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV
WGS
updated 10 months ago by
Ram
43k • written 6.7 years ago by
zhang248
▴ 40
4
votes
6
replies
1.0k
views
Python script to automatically read in, name output files & parse R1 & R2 fastq.gz files when given an input directory with raw data files
python
fastq
9 months ago by
eorr
▴ 30
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
4
votes
6
replies
1.1k
views
Pre-processing for single cell RNAseq: Hard thresholds, data (cluster)-driven or both?
scRNA-seq
updated 6 months ago by
yl759
▴ 120 • written 7 months ago by
psm
▴ 130
4
votes
7
replies
1.4k
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
141k • written 9 months ago by
LeandroF.
• 0
4
votes
12
replies
7.7k
views
6 follow
BWA error: no ID within the read group line
bwa
readgroups
RG
parallel
updated 11 weeks ago by
mgdrnl
▴ 10 • written 3.4 years ago by
whb
▴ 60
4
votes
13
replies
1.0k
views
Mapping FASTQ files of scRNA-seq to reference genome
star
EBI
cellranger
scRNA-seq
SRA
updated 3 months ago by
Ram
43k • written 3 months ago by
Researcher
▴ 20
4
votes
5
replies
775
views
Does adding reads cause batch effects?
kallisto
RNAseq
10 months ago by
bioinfo
▴ 150
4
votes
4
replies
789
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 11 months ago by
Joe
21k • written 11 months ago by
antoine.fauchois92
▴ 20
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 29 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
4
votes
16
replies
954
views
hisat2 location does not exist
hisat2
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Eric
• 0
4
votes
5
replies
1.0k
views
VEP run with --af_gnomadg refuses to provide allele frequencies for extremely rare variants
vep
gnomad
updated 8 months ago by
Louisse_Ensembl
▴ 60 • written 8 months ago by
Jeremy Leipzig
22k
4
votes
14
replies
1.1k
views
remove white space in fastq file
fastq
updated 4 months ago by
GenoMax
141k • written 4 months ago by
gkarere
• 0
3
votes
5
replies
1.1k
views
kraken2 bacteria database 250GB+
metagenomics
16s
kraken2
kraken
updated 5 months ago by
GenoMax
141k • written 5 months ago by
10mz1
▴ 10
3
votes
4
replies
1.0k
views
R package DESeq2 in R 3.5.1
R
updated 11 months ago by
Ram
43k • written 15 months ago by
sehriban.buyukkilic
▴ 10
3
votes
7
replies
3.2k
views
vcf filter for FORMAT argument (DP/GQ/GQX > 30) multiple (380) vcf file
vcffilter
vcftools
sequencing
updated 10 months ago by
Ram
43k • written 4.1 years ago by
IndyDNA
▴ 10
3
votes
1
reply
406
views
Best Tools and Practices for CNV Variant Calling in WES Data
CNV
WES
updated 7 months ago by
Pierre Lindenbaum
161k • written 7 months ago by
Nadav
▴ 20
3
votes
5
replies
528
views
How to assess the quality of the assembly of unmapped reads ?
Pangenome
Iterative-assembly
12 weeks ago by
Sony
▴ 10
3
votes
5
replies
873
views
Optimal number of features to use when integrate multi samples by Seurat in scRNAseq
scRNASeq
Seurat
updated 7 months ago by
Ram
43k • written 7 months ago by
alwayshope
▴ 40
3
votes
6
replies
2.1k
views
Biopython TimeExceptionError how to handle?
biopython
entrez
updated 11 months ago by
Ram
43k • written 6.5 years ago by
Xylanaser
▴ 80
3
votes
6
replies
3.2k
views
samtools sort not working when using multiple threads
samtools
bam
updated 10 months ago by
Ram
43k • written 2.2 years ago by
bio_elle
▴ 10
3
votes
6
replies
709
views
No genes mapped in clusterprofiler gseGO
R
clusterProfiler
gseGO
GSEA
4 months ago by
jon50250
• 0
3
votes
7
replies
482
views
How does kallisto handle multi mapped reads?
kallisto
updated 8 weeks ago by
dsull
★ 5.8k • written 9 weeks ago by
bioinfo
▴ 150
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Star
▴ 60
3
votes
4
replies
4.1k
views
What are the Pros and Cons of working in Bioinformatics???
career
bio
updated 11 months ago by
Ram
43k • written 6.2 years ago by
scottschu97
▴ 20
3
votes
3
replies
2.8k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 7 months ago by
Ram
43k • written 2.6 years ago by
Anand
▴ 40
3
votes
1
reply
517
views
Are there pipelines to analyze the Quality Controls for ATAC-seq and ChIP-seq data?
ChIP-seq
ATAC-seq
updated 9 months ago by
Papyrus
★ 2.9k • written 9 months ago by
Dan
▴ 180
3
votes
4
replies
3.4k
views
Switch ref/alt alleles vcf file
SNP
vcf
sequencing
updated 3 months ago by
jvt
• 0 • written 4.4 years ago by
mdstep
▴ 20
3
votes
4
replies
1.0k
views
Ballgown DE analysis
R
ballgown
Differential-expression
updated 8 months ago by
Ram
43k • written 2.3 years ago by
iamsmor
• 0
3
votes
2
replies
322
views
Illumina reads to be processed and prepared for reference genome alignment
genome
alignment
trimming
next-gen
Illumina
updated 3 months ago by
shelkmike
★ 1.2k • written 3 months ago by
Veselina
• 0
3
votes
6
replies
1.3k
views
how to get total read count, mapped read count and unmapped read count from multiple sam or bam files
RNAseq
PYTHON
R
bash
updated 11 months ago by
Ram
43k • written 3.6 years ago by
Bioinfonext
▴ 460
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length
Bed
updated 10 months ago by
Ram
43k • written 4.2 years ago by
Ankit
▴ 500
3
votes
6
replies
786
views
Annotating genome based on Sequence
genome
annotation
updated 5 months ago by
Darked89
4.6k • written 5 months ago by
buhbs
▴ 30
3
votes
1
reply
544
views
chromosome location to gene name and aa change
variant-annotation
11 months ago by
Zi
• 0
3
votes
5
replies
632
views
ATAC-Seq and featureCounts
ATAC-Seq
featureCounts
updated 3 months ago by
ATpoint
82k • written 3 months ago by
qudrat.nii
▴ 10
3
votes
4
replies
756
views
Should we update time periods in a Bibliometric analysis even after completing it, if it's found to be generating biased results due to recent study?
review
bibliometric
offtopic
8 weeks ago by
Md. Al - Mustanjid
▴ 30
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
1,000 results • Page
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Recent Votes
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
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Recent Replies
Comment: To get p-values for the TPM
by
VITALA
• 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
Comment: alignment result
by
ahmad.sajad4541
• 0
Thank you so much. Should i proceed for annotation step?
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
Answer: Network Alignment
by
Scooter
▴ 280
Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
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by
ZhangYuanfeng
• 0
JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
Comment: PCA plot (Suggestions Needed)
by
Aaliya
▴ 10
I have actually used DESeq2 data.
Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
Dateline
• 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq
by
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87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies
by
Kevin Blighe
87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
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Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
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by
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Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
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