Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
702 results • Page
2 of 15
Sort: Views
Rank
Views
Votes
Replies
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 13 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
23 days ago by
anna
▴ 20
3
votes
6
replies
2.1k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 26 days ago by
Ram
44k • written 2.4 years ago by
SYOSY
▴ 10
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 7 days ago by
Ram
44k • written 3.9 years ago by
millere
• 0
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 17 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 19 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 1 day ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
7 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 14 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 19 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 14 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 3 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 24 days ago by
Gordon Smyth
★ 7.2k • written 8 months ago by
Calum
▴ 10
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 9 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 26 days ago by
bk11
★ 2.5k • written 11 weeks ago by
Sofia
• 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 14 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
17 days ago by
Zhenyu Zhang
★ 1.2k
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
20 days ago by
eebloom
▴ 80
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
17 days ago by
Ibrahim Tanyalcin
★ 1.2k
2
votes
3
replies
1.1k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
updated 1 day ago by
finch
• 0 • written 19 months ago by
Aspire
▴ 330
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 2 days ago by
Ram
44k • written 5 months ago by
LauferVA
4.2k
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
28 days ago by
DKA
▴ 40
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 23 days ago by
jkbonfield
★ 1.2k • written 5 weeks ago by
me
• 0
13
votes
14
replies
1.0k
views
High Malat-1 expression in single cell data
single-cell
updated 14 days ago by
t.montserrat.ayuso
▴ 40 • written 23 days ago by
carolofharvest
▴ 40
7
votes
16
replies
996
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
23 days ago by
Ruqaiya
• 0
1
vote
8
replies
982
views
Adding CB tag to bam file
samtools
bam
updated 27 days ago by
Pierre Lindenbaum
162k • written 4 weeks ago by
Maria
• 0
2
votes
5
replies
966
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 23 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
2
votes
9
replies
966
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 29 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
4
votes
11
replies
924
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
1 day ago by
J
▴ 10
1
vote
10
replies
917
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 16 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
4
votes
11
replies
917
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 29 days ago by
LauferVA
4.2k • written 4 weeks ago by
dominickd
• 0
0
votes
2
replies
879
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 28 days ago by
barslmn
★ 2.2k • written 2.9 years ago by
jhy
▴ 10
2
votes
3
replies
876
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 18 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
1
vote
3
replies
872
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes
imputation
SNP
updated 1 hour ago by
David-walson
• 0 • written 16 months ago by
Apprentice
▴ 160
10
votes
14
replies
842
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 15 days ago by
GenoMax
142k • written 21 days ago by
nicole.kavanagh
• 0
4
votes
6
replies
826
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 25 days ago by
dsull
★ 6.0k • written 29 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
818
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
1
vote
3
replies
812
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 6 days ago by
sansan_96
▴ 90 • written 2.8 years ago by
boymin2020
▴ 80
0
votes
1
reply
810
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 20 days ago by
Ram
44k • written 2.7 years ago by
carov
• 0
1
vote
8
replies
803
views
Random Access remote BAM files
htslib
BAM
updated 5 hours ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 10
1
vote
16
replies
802
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 4 days ago by
GenoMax
142k • written 7 days ago by
hophuquy0944
• 0
8
votes
8
replies
797
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 27 days ago by
swbarnes2
14k • written 28 days ago by
Aaliya
▴ 10
0
votes
1
reply
789
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 24 days ago by
Francesco
▴ 10 • written 3.4 years ago by
gt
▴ 30
0
votes
3
replies
787
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 23 days ago by
weidonglu
• 0 • written 22 months ago by
JZX
• 0
2
votes
11
replies
785
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
5 days ago by
egascon
• 0
2
votes
9
replies
779
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 7 days ago by
Pierre Lindenbaum
162k • written 15 days ago by
schmince
• 0
1
vote
6
replies
769
views
anRichment is missing
WGCNA
anRichment
updated 16 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
0
votes
2
replies
760
views
homer not configured properly
Homer
makeTagDirectory
updated 20 days ago by
clairechung112
• 0 • written 2.0 years ago by
amahdi779
• 0
3
votes
8
replies
746
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 16 days ago by
Chris Dean
▴ 410 • written 20 days ago by
sovrappensiero
▴ 100
5
votes
4
replies
745
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
28 days ago by
kirillkirilenko
▴ 40
702 results • Page
2 of 15
Recent Votes
Error when looping over multiple columns in a data frame in R
Answer: Microbial community analysis pipelines in metagenomics
A: What are chimeric reads?
Answer: Allele count of 2 for homoplasmic MT variants in VCF
Find count of reads in BAM file that fall within BED region
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Recent Locations •
All
United States,
8 minutes ago
Hong Kong,
11 minutes ago
Perth, Australia,
15 minutes ago
Hong Kong,
16 minutes ago
Australia,
18 minutes ago
Hong Kong,
23 minutes ago
Hong Kong,
24 minutes ago
Recent Awards •
All
Scholar
to
LChart
3.9k
Scholar
to
ATpoint
82k
Popular Question
to
liyong
▴ 80
Popular Question
to
Shicheng Guo
★ 9.4k
Popular Question
to
reza
▴ 300
Popular Question
to
mhale
▴ 20
Teacher
to
Ashutosh Pandey
12k
Recent Replies
Comment: samtools write-index
by
LucisTheFather
• 0
``` -o alignment.sorted.bam##idx##alignment.sorted.bam.bai ``` This portion is to get .bai index, instead of .csi indexing. Although Idk th…
Comment: samtools write-index
by
LucisTheFather
• 0
Really appreciate your help Pierre! I am a little bit confused btw. do you mean this: ``` rm -vf alignment.sorted.bam.bai minimap2 -ax map-…
Comment: samtools write-index
by
LucisTheFather
• 0
Yeah, I did multiple split tests of my pipeline (just subset 400k rows of my fastq and run through my pipeline for quick tests) and none of…
Comment: Which 1000 genomes 30x files should I use for imputation?
by
David-walson
• 0
Hi there. Have you found any suggestions? I have alos been working on the 1KGP high coverage data, but i have no idea about how to use it p…
Comment: MAUVE: No gene annotations in Genbank file alignments
by
pramach1
▴ 40
The same problem persists for me too. Running progressiveMauve on command line on bunch of gbk files. Mauve itself runs fine and I do see t…
Answer: Error when looping over multiple columns in a data frame in R
by
Jeremy
▴ 910
First of all, you should use "tag.healthy" and "methods" instead of "tag.health" and "method". Also, optimal.cutpoints() wants X to be eit…
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Past thread: https://www.biostars.org/p/178266/
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Mouse bodymap samples : https://ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375882%20&o=acc_s%3Aa
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
bk11
★ 2.5k
Here is the [RatGTEx][1] [1]: https://ratgtex.org
Comment: Random Access remote BAM files
by
a.penatauber
• 0
Hi Lucas, I am looking for a similar functionality as I'm working with a large volume of CRAM files on S3, and downloading them whole would…
Comment: from CRAM to fastq
by
ATpoint
82k
Yes, but I still think that with this syntax you get an uncompressed file, because samtools does not detect the gz suffix. Just take a `hea…
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
Overlap of "Ch1 200 250" and "Ch1 150 220" is "Ch1 200 220", but I want to combine windows that have overlap. Thus, my goal is to combine …
Comment: Flag multiple filtering steps on VCF files using VEP
by
Pierre Lindenbaum
162k
I don't understand that question.
Comment: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> But your answer is exactly the opposite of what I want oh I see. but i don't understand the logic why: "Ch1 200 250" and "Ch1 150 220" …
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
sorry i edited my example. But your answer is exactly the opposite of what I want
Traffic: 1735 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6