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700 results • Page
2 of 14
Sort: Views
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Views
Votes
Replies
6
votes
5
replies
2.4k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 16 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 14 days ago by
Ram
44k • written 13 months ago by
mohyeddine.taleb
• 0
3
votes
7
replies
2.3k
views
Tool:
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart
annotation
Ensembl
updated 10 hours ago by
Ram
44k • written 2.8 years ago by
Shred
★ 1.4k
19
votes
15
replies
2.3k
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 7 days ago by
Mohamed
• 0 • written 8 months ago by
vincenthus
▴ 70
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 25 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
0
votes
6
replies
2.2k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 19 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
29 days ago by
anna
▴ 20
2
votes
6
replies
2.0k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 13 days ago by
Ram
44k • written 3.9 years ago by
millere
• 0
6
votes
6
replies
1.9k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 23 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 25 days ago by
e.r.zakiev
▴ 210 • written 3.9 years ago by
n.anuragsharma
▴ 40
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 7 days ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
6
votes
5
replies
1.8k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
14 days ago by
Arton
▴ 10
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 20 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 25 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
2
votes
7
replies
1.6k
views
Problems when trying to use ensembl-vep
ensembl
ensembl-vep
docker
updated 21 hours ago by
tomas4482
▴ 400 • written 10 months ago by
langziv
▴ 50
3
votes
9
replies
1.5k
views
Rseqc infer_experiment.py: 0 usable reads sampled and unknown data type
rseqc
infer_experiment.py
RNA-seq
updated 4 hours ago by
mazegriff
• 0 • written 17 months ago by
pubsurfted
▴ 40
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 20 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 9 days ago by
scideas
▴ 30 • written 9 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 15 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 20 days ago by
chenl
▴ 10 • written 2.6 years ago by
Martyna
• 0
1
vote
2
replies
1.2k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
23 days ago by
Zhenyu Zhang
★ 1.2k
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
5 days ago by
Aspire
▴ 330
1
vote
4
replies
1.2k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
26 days ago by
eebloom
▴ 80
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 8 days ago by
Ram
44k • written 5 months ago by
LauferVA
4.2k
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
23 days ago by
Ibrahim Tanyalcin
★ 1.2k
13
votes
14
replies
1.1k
views
High Malat-1 expression in single cell data
single-cell
updated 20 days ago by
t.montserrat.ayuso
▴ 40 • written 29 days ago by
carolofharvest
▴ 40
2
votes
4
replies
1.1k
views
samtools mpileup error - 1 samples in 1 input files
samtools
BAM
mpileup
SAM
updated 1 day ago by
Damla
• 0 • written 2.5 years ago by
joseph.kelly.94
▴ 10
2
votes
11
replies
1.1k
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 29 days ago by
jkbonfield
★ 1.2k • written 5 weeks ago by
me
• 0
7
votes
16
replies
1.1k
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
29 days ago by
Ruqaiya
• 0
2
votes
5
replies
976
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 29 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
4
votes
11
replies
969
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
7 days ago by
J
▴ 10
1
vote
10
replies
930
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 22 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
1
vote
3
replies
915
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes
imputation
SNP
updated 6 days ago by
David-walson
• 0 • written 16 months ago by
Apprentice
▴ 160
2
votes
3
replies
897
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 24 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
10
votes
14
replies
891
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 21 days ago by
GenoMax
142k • written 27 days ago by
nicole.kavanagh
• 0
3
votes
8
replies
886
views
Random Access remote BAM files
htslib
BAM
updated 6 days ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 20
3
votes
3
replies
864
views
Cut&Run and heatmap
MACS2
bowtie2
updated 13 hours ago by
Ram
44k • written 13 months ago by
qudrat.nii
▴ 10
7
votes
13
replies
851
views
7 follow
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 5 days ago by
i.sudbery
19k • written 5 weeks ago by
Estevão
▴ 10
1
vote
16
replies
846
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 10 days ago by
GenoMax
142k • written 13 days ago by
hophuquy0944
• 0
1
vote
5
replies
829
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
1
vote
3
replies
824
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 12 days ago by
sansan_96
▴ 90 • written 2.8 years ago by
boymin2020
▴ 80
2
votes
11
replies
819
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
11 days ago by
egascon
• 0
0
votes
1
reply
816
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 26 days ago by
Ram
44k • written 2.7 years ago by
carov
• 0
2
votes
9
replies
813
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 13 days ago by
Pierre Lindenbaum
162k • written 21 days ago by
schmince
• 0
2
votes
11
replies
798
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 2 days ago by
Ram
44k • written 11 days ago by
hannes.bongartz
• 0
1
vote
6
replies
797
views
anRichment is missing
WGCNA
anRichment
updated 22 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
0
votes
3
replies
795
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 29 days ago by
weidonglu
• 0 • written 22 months ago by
JZX
• 0
0
votes
1
reply
784
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 23 days ago by
GenoMax
142k • written 24 days ago by
tulip
• 0
3
votes
8
replies
774
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 22 days ago by
Chris Dean
▴ 410 • written 26 days ago by
sovrappensiero
▴ 100
0
votes
2
replies
767
views
homer not configured properly
Homer
makeTagDirectory
updated 26 days ago by
clairechung112
• 0 • written 2.0 years ago by
amahdi779
• 0
700 results • Page
2 of 14
Recent Votes
Answer: when I use htslib to write a bam. Error of "truncated file" shows by samtools
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Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
update. The error persists. With ValidateSamFile I get no error until i use MarkDuplicates. Then for the MarkDuplicates output I get: …
Comment: when I use htslib to write a bam. Error of "truncated file" shows by samtools
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Thanks very much.
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4.2k
Hello @ab33b6d7 , Below is approximately the code block you provided, with a few additional lines added. Each of the new lines has > …
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Comment: Rseqc infer_experiment.py: 0 usable reads sampled and unknown data type
by
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Hi pubsurfted, I ran into the same issue using a reference transcriptome with HISAT2 from the Ensembl database. For others with similar e…
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isec is pretty awful for these set operations - especially since individual samples present alleles, not lines in a VCF file. If you can co…
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Maybe try to calculate min and max combined_min <- min(a_filtered$value, a_filtered_tv$value, na.rm = TRUE) combined_max <- max(a_…
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Use `+ylim(c(lower, upper))`. Either set manually, or query both `a_filtered` and `a_filtered_tv` for the minimum and maximum values that g…
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I am not familiar with deseq data, but if it makes sense, remove rows/columns that have only NAs. #remove rows x<- mat.z[ rowSums(…
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There are several problems with this code: 1. You have not set `b->l_data`, which here should be set to the same value as `b->m_data`. T…
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How come? If I have a pro-tumorigenic product, for example, wouldn't this comparison be valid?
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Thanks @Zhenyu Zhang for your response. I have just looked at the files you mentioned. Do you have any recommended package or code snippet …
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As far I understand non coding region equal to the intergenic region? please can you write an example for how to calculate one region ? I…
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In the GDC, there are raw float value CNV data, and integer CNV values after advanced modeling. If you only want those floating-point numbe…
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