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
122,202 results • Page
682 of 2445
Sort: Rank
Rank
Views
Votes
Replies
0
votes
1
reply
1.5k
views
TMM normalization for data across two sequencing batches
tmm
normalization
rnaseq
updated 4.6 years ago by
ATpoint
90k • written 4.6 years ago by
wiscoyogi
▴ 40
2
votes
2
replies
1.5k
views
Why we have exons that start and end at the same coordinate?!
gtf
exon
GRCh38
updated 4.6 years ago by
WouterDeCoster
48k • written 4.6 years ago by
Medhat
9.8k
2
votes
3
replies
1.2k
views
Microarray Error
R
Microarray
4.6 years ago by
rpazo001
▴ 20
4
votes
7
replies
2.7k
views
Genotype Data in PLINK
Genotype
PLINK
updated 4.6 years ago by
Sam
★ 4.8k • written 4.6 years ago by
carlstat123
• 0
8
votes
2
replies
1.4k
views
How to extract fasta sequences and only its ID's, based on the subsequence fasta numbers from a main fasta file ?
fasta
RNA
DNA
alignment
updated 4.6 years ago by
cpad0112
21k • written 4.6 years ago by
sunnykevin97
▴ 1000
0
votes
0
replies
740
views
Creating a comparison sequence for Multiple sequence alignment in Artemis Comparison Tool (ACT)
multiplesequencealignment
artemis
updated 4.6 years ago by
h.mon
35k • written 4.6 years ago by
Joel
• 0
0
votes
0
replies
1.0k
views
Calculate weighted and unwieghted Unifrac
R
MEGA
Unifrac
4.6 years ago by
chiara.conte91
• 0
0
votes
0
replies
730
views
Error in discretizeDF.supervised(formula, data, method = disc.method) :data needs to be a data.frame
R
arulesCBA
4.6 years ago by
hebasamysaeid1
• 0
1
vote
3
replies
1.7k
views
Testing independence between 5' and 3' terminal sequences in a DNA database
sequence
cluster
DNA
independence
testing
updated 4.6 years ago by
Istvan Albert
103k • written 4.6 years ago by
Anand Rao
▴ 650
1
vote
0
replies
1.5k
views
Job:
Bioinformatics Research Analyst - Oncology
oncology
genomics
4.4 years ago by
Malachi Griffith
20k
7
votes
4
replies
4.7k
views
Visualizing & plotting variant reads within BAM files programmatically?
alignment
4.6 years ago by
steve
★ 3.5k
0
votes
0
replies
613
views
Is there any method or algorithm to identify mutation using gene expression information?
algorithm
mutation
4.6 years ago by
Rida
• 0
4
votes
6
replies
2.0k
views
How to extract sub fasta sequences from a multiline fasta file ?
RNA
DNA
4.6 years ago by
sunnykevin97
▴ 1000
7
votes
5
replies
8.2k
views
How to convert multiple vcf files to a ped file?
plink
vcftools
updated 4.6 years ago by
Medhat
9.8k • written 9.2 years ago by
line1438
▴ 40
0
votes
0
replies
955
views
News:
Online training: Data Visualization with Python
Python
DataVisualization
4.6 years ago by
Physalia-courses
★ 2.7k
2
votes
1
reply
890
views
Phylip/Paml alignment output file explanation ?
RNA
alignment
DNA
updated 4.6 years ago by
Dave Carlson
★ 2.2k • written 4.6 years ago by
sunnykevin97
▴ 1000
2
votes
8
replies
2.4k
views
BWA mapping quality 0 for all reads
mapping
mapping_quality
bwa
updated 4.6 years ago by
Istvan Albert
103k • written 4.6 years ago by
OhHiImNewHere
▴ 10
0
votes
1
reply
1.6k
views
Pathway enrichment with z-scores
Transcriptomics
GSEA
NGS
updated 4.6 years ago by
jared.andrews07
★ 19k • written 4.6 years ago by
glady
▴ 320
0
votes
0
replies
833
views
Job:
Biostatistician Job Opportunity (Bethesda, MD)
Genomics
statistics
Analysis
Rstudio
4.6 years ago by
christmasy
• 0
1
vote
1
reply
5.2k
views
Removing duplicate varaints in PLINK
plink
updated 4.6 years ago by
lax
▴ 30 • written 4.6 years ago by
f-rasmussen
▴ 10
1
vote
2
replies
1.3k
views
How to get Python code to run correctly for hetero-dimerization analysis
python
sequence
programming
FASTA
updated 4.6 years ago by
cpad0112
21k • written 4.6 years ago by
Apex92
▴ 320
11
votes
6
replies
2.3k
views
Forum:
Is it still interesting to publish the profile of the transcriptome?
Article
RNA
Transcriptome
Suggestion
RNAseq
4.6 years ago by
tiagobellintani
▴ 40
1
vote
3
replies
1.5k
views
How to extract de novo transcript from RNA long read alignement ?
RNA
pacbio
updated 4.6 years ago by
Juke34
9.3k • written 4.6 years ago by
sacha
★ 2.5k
4
votes
9
replies
9.2k
views
GATK Mutect2 Panel-Of-Normals generation
gatk
mutect2
panel-of-normal
wes
non-tumor
updated 4.6 years ago by
DIG
• 0 • written 5.4 years ago by
cocchi.e89
▴ 300
3
votes
4
replies
1.4k
views
How to split the header line into its components
Macspider
updated 4.6 years ago by
cpad0112
21k • written 4.6 years ago by
Inayat
• 0
1
vote
0
replies
853
views
how to tell the OR or BETA in the OR.or.BETA column in GWAS summary statistics from GWAS catalog?
gwassummary
gwascatalog
4.6 years ago by
zhoufeng2ye
▴ 10
0
votes
3
replies
1.7k
views
Multiple motif [available in .txt file ] search from large fasta file to find motif frequency then print fasta sequences
motif
fasta
frequency
4.6 years ago by
Swarna Kanchan
▴ 10
2
votes
2
replies
1.4k
views
how to have aligned region in fasta format using blastn?
blastn
fasta
updated 4.5 years ago by
Ram
45k • written 4.6 years ago by
mthm
▴ 80
0
votes
4
replies
2.6k
views
Help with salmon quantification of samples with de novo transcriptome
salmon
denovo
tximport
updated 4.6 years ago by
ponganta
▴ 590 • written 4.6 years ago by
codyas
• 0
2
votes
0
replies
1.0k
views
what are the parameters we should change when we run VariantsToTable of GATK in splitting multi allelic mode?
variantstotable
gatk
vcf
picard
4.6 years ago by
DareDevil
★ 4.5k
0
votes
0
replies
451
views
fetching first column as a class attribute in arulesCBA
arulesCBA
R
4.6 years ago by
hebasamysaeid1
• 0
1
vote
4
replies
2.3k
views
MA plots with similar distribution but display difference in significantly expressed genes
reads
MAplot
DEG
rna
DESeq2
updated 4.6 years ago by
seidel
11k • written 4.6 years ago by
fufor94
▴ 10
1
vote
1
reply
1.4k
views
PCA plot making
VCF
PCA
vcftools
SNP
updated 4.6 years ago by
prasundutta87
▴ 730 • written 4.6 years ago by
yb87625
• 0
1
vote
0
replies
1.1k
views
Could it be risky to analyse cells that are negative after cell hashing on single cell RNA sequencing?
RNA-Seq
singlecell
R
Seurat
4.6 years ago by
charlesgwellem
▴ 10
0
votes
0
replies
1.1k
views
CNVkit flat reference file creation
CNV
ces
Flatreference
CNVkit
wes
4.6 years ago by
enes
▴ 40
10
votes
4
replies
9.6k
views
What is gnomAD allele frequency
AF
gnomAD
updated 22 months ago by
Lhl
▴ 760 • written 4.6 years ago by
Eric Wang
▴ 70
2
votes
3
replies
2.2k
views
Remove reads from bam file that partially covers a region
indel
filter
bam
4.6 years ago by
arbarharw
• 0
0
votes
3
replies
1.2k
views
Trim alignment from .sam file based on a specific tab-delimiter .bed file
sam
updated 4.6 years ago by
Pierre Lindenbaum
166k • written 4.6 years ago by
khanhlpbao
• 0
0
votes
0
replies
805
views
SNP Mapping/Characterisation and Patches
GRCh38
prioritisation
patches
SNP
4.6 years ago by
KBMP
• 0
0
votes
2
replies
1.3k
views
Help with statistic model
online
education
R
updated 4.6 years ago by
Kevin Blighe
★ 90k • written 4.6 years ago by
Bioman
• 0
1
vote
2
replies
2.5k
views
Convert multiple rows value retrieved from ensemble biomart to comma separated list for a common ensemble gene ID.
ensembl
Biomart
R
geneontology
updated 4.4 years ago by
Ram
45k • written 4.6 years ago by
sontiroy
• 0
0
votes
0
replies
1.0k
views
UCSC parameters for converting between human genome builds
genomics
bed
ucsc
genotyping
4.6 years ago by
jon.klonowski
▴ 210
5
votes
3
replies
1.9k
views
RNA-SEQ count data as input for Machine Learning
machine
learning
rnaseq
normalize
updated 4.6 years ago by
Dunois
★ 2.9k • written 4.6 years ago by
Alberto
• 0
2
votes
5
replies
2.0k
views
Extracting only tumor samples from Single cell RNASeq
tumor
cell
singel
RNA
updated 4.6 years ago by
jared.andrews07
★ 19k • written 4.6 years ago by
David_emir
▴ 500
9
votes
6
replies
2.3k
views
6 follow
What are some areas where machine learning is applicable in biology and cancer?
software
deep learning
updated 4.6 years ago by
krysgourlia
▴ 30 • written 5.9 years ago by
isaacbruth1234
• 0
6
votes
11
replies
3.1k
views
How are transcriptome annotations published?
RNAseq
annotation
publish
transcriptome
4.3 years ago by
Dunois
★ 2.9k
0
votes
2
replies
1.1k
views
Hetero-dimerization analysis with two FASTA files
sequence
FASTA
python
awk
bash
updated 4.6 years ago by
Ram
45k • written 4.6 years ago by
Apex92
▴ 320
3
votes
4
replies
2.1k
views
Convert per base bedgraph to Bed format
Bedgraph
perbase
Bed
Bedtools
updated 4.6 years ago by
Alex Reynolds
36k • written 4.6 years ago by
bioyas
▴ 20
5
votes
4
replies
12k
views
Why is `send` lower than `sstart` from blast format 6 output?
blast
genomics
updated 4.6 years ago by
David
• 0 • written 5.8 years ago by
O.rka
▴ 750
0
votes
0
replies
1.2k
views
bcftools isec not producing sites.txt
bcftools
4.6 years ago by
steve
★ 3.5k
122,202 results • Page
682 of 2445
Recent Votes
Comment: low quality data or file name swapping -- cellranger arc errors when processing
Comment: low quality data or file name swapping -- cellranger arc errors when processing
A: Regarding Microarray Platforms
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Recent Locations •
All
United Kingdom,
just now
Germany,
3 minutes ago
Bologna,
11 minutes ago
Taiwan,
18 minutes ago
Qatar,
29 minutes ago
Leipzig, Germany,
40 minutes ago
Hong Kong,
50 minutes ago
Recent Awards •
All
Popular Question
to
Lila M
★ 1.3k
Popular Question
to
ecSeq Bioinformatics
▴ 20
Popular Question
to
QX
▴ 80
Teacher
to
dthorbur
★ 3.2k
Popular Question
to
colindaven
8.1k
Teacher
to
ATpoint
90k
Popular Question
to
san96
▴ 190
Recent Replies
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
• 0
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
• 0
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Comment: 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
• 0
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…
Comment: Can i use orthofinder for small protein datasets and not full proteome?
by
alexandrakortsi
• 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
xinguok794
▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics
by
Kent
▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Traffic: 3506 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