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 : all time
all time
today
this week
this month
this year
122,213 results • Page
709 of 2445
Sort: Rank
Rank
Views
Votes
Replies
1
vote
5
replies
1.9k
views
GATK VCF output: where are the sample-level annotations?
SNP
sequence
GATK
VCF
4.7 years ago by
mcrepeau
▴ 20
4
votes
5
replies
1.9k
views
Extracting CDS from fragmented assemblies
Assembly
alignment
updated 4.7 years ago by
Carambakaracho
★ 3.3k • written 4.7 years ago by
ebaldwin
▴ 40
3
votes
1
reply
1.7k
views
Tool:
Introducing Gallia: a Scala library for data manipulation
scala
etl
json
vcf
spark
updated 2.5 years ago by
Ram
45k • written 4.8 years ago by
cros.anthony
▴ 30
2
votes
3
replies
4.1k
views
choose specific python version within conda environment
conda
python
4.7 years ago by
AQ7
▴ 30
0
votes
1
reply
993
views
bwa read group tagging failed in PBS cluster
alignment
next-gen
software error
updated 4.7 years ago by
Biostar
20 • written 4.9 years ago by
chenyangkang24
▴ 10
1
vote
0
replies
1.1k
views
Correct Data from TCGA for EdgeR Analysis
rna-seq
4.7 years ago by
joseph.landry
▴ 50
1
vote
5
replies
2.4k
views
Reading multiple txt files and perform Two Sample Mendelian Randomization in R
2 sample MR
Multiple txt files
4.7 years ago by
mscpythonstudy
▴ 20
0
votes
5
replies
2.4k
views
Creating Correlation Plot using distance method from a data.frame
R
correlation
corrplot
updated 4.7 years ago by
Mensur Dlakic
★ 30k • written 4.7 years ago by
jansha.1997
• 0
0
votes
0
replies
724
views
Finding mutational burden in TCGA dataset
genome
python
UTR
tcga
cancer
4.7 years ago by
Jamie Watson
▴ 20
4
votes
5
replies
4.5k
views
Replace fasta Header witha a matching text
awk
seqkit
grep
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
Optimist
▴ 190
0
votes
0
replies
745
views
rmsd graph equilibrium
MD Simulation
rmsd
4.7 years ago by
prinebula23
• 0
0
votes
1
reply
598
views
Error while running the transcript count file obtained using StringTie on DeSeq2
R
sequencing
software error
4.7 years ago by
vedant23081998
• 0
2
votes
4
replies
1.6k
views
Isoform detection of a gene using RNAseq
RNA-Seq
isoform_detection
4.7 years ago by
vinishavvenugopal
▴ 30
0
votes
0
replies
678
views
ViewBS error in visualizing BSSeq data
Bisulfite
sequencing
Analysis
software error
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
abseq
▴ 10
0
votes
1
reply
858
views
Extract features from fasta sequences
fasta
feature-extraction
machine-learning
4.7 years ago by
suresh.wrc
• 0
6
votes
4
replies
5.3k
views
Forum:
Chip-Seq Data Analysis
chip-seq
updated 2.8 years ago by
Ram
45k • written 13.5 years ago by
Raony Guimarães
★ 1.5k
9
votes
10
replies
21k
views
6 follow
GO analysis- analyze upregulated and downregulated genes separately?
RNA-Seq
updated 3.2 years ago by
Ram
45k • written 10.3 years ago by
ssukumaran
▴ 30
3
votes
2
replies
1.2k
views
Job:
Need Transcriptome bioinformatician's collaboration
next-gen-sequencing
R
RNA-seq
alignment
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
s.mojtabaghiasi
▴ 20
35
votes
22
replies
26k
views
13 follow
Renaming fasta headers according to a matching name list
text-processing
command-line
sequence
updated 3.7 years ago by
Priya
▴ 20 • written 9.7 years ago by
san.san
▴ 190
3
votes
2
replies
1.0k
views
Order a chromsome assembly with a chromosome assembly of a closely related species/
assembly
genome
updated 4.7 years ago by
lieven.sterck
16k • written 4.7 years ago by
cdjeu
▴ 10
2
votes
3
replies
2.6k
views
Deeptools plotHeatmap values
Deeptools
plotHeatmap
ChIP-Seq
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
saha.shagnik
• 0
1
vote
6
replies
2.2k
views
GATK issue in running Mutect2
next-gen
snp
updated 4.7 years ago by
2nelly
▴ 350 • written 4.8 years ago by
jyotsana18237
• 0
7
votes
9
replies
10k
views
6 follow
Getting mitochondrial genes for scRNAseq
RNA-Seq
rna-seq
scRNAseq
single-cell
updated 4.7 years ago by
charlesgwellem
▴ 10 • written 5.4 years ago by
m-harbus
• 0
1
vote
4
replies
2.2k
views
Correspondence between unlabeled/different tips of different phylogenetic trees
Phylogenetics
Trees
gene
sequence
updated 4.7 years ago by
Biostar
20 • written 7.7 years ago by
rfm
• 0
0
votes
0
replies
678
views
lncRNA-target reference file with proper gene nomenclature
gene
genome-sequencing
lincRNA
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
Apex92
▴ 320
0
votes
1
reply
870
views
Getting ENTREZ GENE IDs for data frame, any help?
R
gene
Assembly
updated 4.7 years ago by
cpad0112
21k • written 4.7 years ago by
ymervenuryavuz
• 0
0
votes
1
reply
776
views
Regression - correcting for the same covariate with a different value twice
regression
age-correction
R
4.7 years ago by
ika
▴ 50
0
votes
4
replies
1.5k
views
How to draw survival curve marked at one censoring time for each patient
R
survival
kaplan-meier
updated 4.7 years ago by
zx8754
12k • written 4.7 years ago by
Apprentice
▴ 190
2
votes
2
replies
1.0k
views
Plink1.07 generate ERRORs when reading covaries
SNP
plink
updated 4.7 years ago by
zx8754
12k • written 4.7 years ago by
heqianchange
▴ 10
0
votes
3
replies
1.1k
views
get coordinates for a list of genes
RNA-Seq
gene
updated 4.7 years ago by
zx8754
12k • written 4.7 years ago by
robinycfang
▴ 20
12
votes
15
replies
3.5k
views
6 follow
Is there other IDE like R studio working on the linux?
bioconductor
Rstudio
R
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
shangguandong1996
▴ 30
2
votes
1
reply
1.0k
views
Ensembl REST to download transcript fastas
ensembl
updated 4.7 years ago by
Emily
24k • written 4.7 years ago by
H Miller
• 0
0
votes
0
replies
1.2k
views
Converting 1kHG genomic coordinates from hg37 to hg38 build
python3
CrossMap
1kHG
hg37 to hg38
4.7 years ago by
AVA
▴ 40
3
votes
3
replies
1.5k
views
scRNA analysis in PDX model
NGS
PDX
scRNA
4.6 years ago by
leedakyung1998
▴ 10
1
vote
0
replies
2.4k
views
How To Query Snp Against Genomic Features In R
snp
genomic
updated 4.7 years ago by
Biostar
20 • written 11.6 years ago by
Zhenyu Zhang
★ 1.3k
0
votes
0
replies
876
views
Identification of presence of genes by aligning the illumina reads to reference genome with Geneious
geneious
alignment
mapping
4.7 years ago by
rthapa
▴ 90
0
votes
1
reply
837
views
KEGG enrichment pathway
KEGG
4.7 years ago by
amoaristotle
• 0
3
votes
1
reply
2.0k
views
Error on Linear regression bulkRNAseq
R
linear
regression
residue
updated 4.7 years ago by
rpolicastro
13k • written 4.7 years ago by
camillab.
▴ 160
0
votes
1
reply
2.0k
views
from phased SNPs to haplotype blocks (or phase sets)
eagle2
statistical phasing
haplotype block
updated 4.7 years ago by
Peter Chung
▴ 210 • written 6.1 years ago by
Nicola Casiraghi
▴ 500
0
votes
0
replies
1.3k
views
where to get PBMC (68k) labels?
pbmc
single-cell
10x
4.7 years ago by
mk
▴ 310
1
vote
8
replies
5.4k
views
PCA plotting using DESEq2 pipeline
RNA-Seq
4.7 years ago by
aranyak111
• 0
4
votes
6
replies
4.1k
views
BWA_MEM error "cannot find file.fa.pac" but input is file.fa
alignment
updated 3.8 years ago by
Karly
• 0 • written 6.1 years ago by
jdk48542
• 0
1
vote
3
replies
6.9k
views
ERROR 127: ABYSS-P: error while loading shared libraries: libmpi.so.40: cannot open shared object file: No such file or directory
abyss
assembly
updated 4.7 years ago by
Biostar
20 • written 8.0 years ago by
freuv
▴ 20
0
votes
0
replies
993
views
Adding information tags with types, positions and counts of matches and mismatches in every read in the SAM file
RNA-Seq
4.7 years ago by
lechu
▴ 20
3
votes
7
replies
7.5k
views
Gene expression heatmap following pseudotime analysis
RNA-Seq
updated 4.7 years ago by
rpolicastro
13k • written 4.8 years ago by
Vitis
★ 2.6k
1
vote
2
replies
1.4k
views
Job:
Looking for a programmer well versed in Cytoscape layouts and JavaScript - Remote contract
cytoscape.js
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
yogish.kode
• 0
1
vote
0
replies
1.5k
views
ssGSEA analysis workflow and interpretation
RNA-Seq
4.7 years ago by
salehm
▴ 10
0
votes
1
reply
711
views
How to download TCGA2STAT package?
R
4.7 years ago by
msndapaah
• 0
0
votes
1
reply
1.5k
views
Confusion of the input format for DESeq2 and EdgeR for bulk- and scRNA-seq
DESeq2
EdgeR
RNA-Seq
scRNA-seq
4.7 years ago by
cwwong13
▴ 40
0
votes
0
replies
1.0k
views
Getting normalized count/ gene expression matrix for both bulk and single-cell RNA-seq
RNA-Seq
scRNA-seq
DESeq2
EdgeR
4.7 years ago by
cwwong13
▴ 40
122,213 results • Page
709 of 2445
Recent Votes
A: PCA in a RNA seq analysis
what cause poly-G from NextSeq
what cause poly-G from NextSeq
A: what cause poly-G from NextSeq
A: what cause poly-G from NextSeq
How to trim transcripts using information from NCBI contamination screen report
How to trim transcripts using information from NCBI contamination screen report
Recent Locations •
All
Tanzania,
21 minutes ago
India/Ahmedabad,
29 minutes ago
United States,
31 minutes ago
India,
41 minutes ago
India,
1 hour ago
Japan,
1 hour ago
United States,
2 hours ago
Recent Awards •
All
Popular Question
to
sahalpaladan
▴ 10
Popular Question
to
Amb@r85
▴ 10
Popular Question
to
hello_bioinf
▴ 250
Popular Question
to
tacrolimus
▴ 150
Popular Question
to
biotrekker
▴ 110
Popular Question
to
zizigolu
★ 4.4k
Popular Question
to
Biomed-jeh
▴ 70
Recent Replies
Answer: How excactly is the Q30 is calculated?
by
GenoMax
154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
Comment: best practice for diploid variant calling
by
Matteo Ungaro
▴ 130
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind
by
ATpoint
90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read
by
cmdcolin
★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets
by
GenoMax
154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
samuel.a.odonnell
▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
Pierre Lindenbaum
166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Traffic: 4112 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