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122,214 results • Page
710 of 2445
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Votes
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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
0
votes
0
replies
915
views
Should "dispersion" in edgeR be calculated for entire dataset or just conditions being analyzed?
differential-gene-expression
edgeR
RNA-Seq
updated 22 months ago by
Ram
45k • written 4.7 years ago by
O.rka
▴ 750
0
votes
1
reply
1.4k
views
Trimming Ion Total RNA-seq Kit v2
RNA-Seq
Ion Torrent
Trimming
Adapters
updated 4.7 years ago by
Biostar
20 • written 4.8 years ago by
drsami
▴ 90
0
votes
1
reply
901
views
DESeq2 for specific genes
deseq2
RNA-Seq
R
specific genes
pathways
updated 4.7 years ago by
swbarnes2
15k • written 4.7 years ago by
andreiareis1987
▴ 40
0
votes
0
replies
734
views
Total number of trimmed reads less than number of mapped reads
alignment
next-gen
sequence
SAMtools
BWA
4.7 years ago by
kspata
▴ 90
1
vote
2
replies
2.0k
views
Select list of nodes in Cytoscape
Cytoscape
Gene Ontology
Biological Network
updated 4.7 years ago by
scooter
▴ 650 • written 4.7 years ago by
qmarulfiz
▴ 60
1
vote
1
reply
1.0k
views
Open Linkout with another web browser
cytoscape
updated 4.7 years ago by
scooter
▴ 650 • written 4.8 years ago by
vahiniaina.andriamanga
• 0
0
votes
0
replies
1.5k
views
Calculating ROHs and Heterozygosity from GATK
ROHs
GATK
Heterozygosity
4.7 years ago by
gubrins
▴ 350
3
votes
5
replies
1.6k
views
Microarray data from different sets but same platform
microarray
R
gene
Affymetrix
updated 4.7 years ago by
ATRX
★ 1.2k • written 4.7 years ago by
Ahmed.waraky
▴ 10
2
votes
3
replies
1.3k
views
want to extract all column which have particular value
extract
awk
updated 4.7 years ago by
ashishjayamohan
• 0 • written 4.7 years ago by
harry
▴ 40
0
votes
2
replies
1.4k
views
On understanding the axis of a PCA plot
pca
updated 4.7 years ago by
Sam
★ 4.8k • written 4.7 years ago by
Aspire
▴ 390
7
votes
8
replies
2.5k
views
[RNA-seq] Extremely Unconsistent Raw Count from Different Tools; a dark mistery
RNA-Seq
alignment
counts
updated 4.7 years ago by
i.sudbery
22k • written 4.7 years ago by
ReWeeda
▴ 120
132
votes
44
replies
47k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 2.7 years ago by
Ram
45k • written 9.2 years ago by
Lars
★ 1.1k
0
votes
0
replies
1.8k
views
Job:
Senior Research Scientist: Bioinformatician specialising in bacterial genomics (Maternity cover)
genome
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
jemma.bruce
• 0
0
votes
1
reply
1.5k
views
Effective subsampling of BAMs
BAM
sampling
updated 4.7 years ago by
ATpoint
90k • written 4.7 years ago by
esimonova.me
▴ 30
0
votes
9
replies
2.4k
views
BBMap not mapping reads to sequences known to exist in reference
alignment
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
robert.murphy
▴ 110
1
vote
2
replies
1.5k
views
Script for XP-EHH, EHH and iHS tests and phasing vcf file that works on all chromosome concurrently
WGS
Pooled-Seq
XPEHH
EHH
iHS
4.7 years ago by
taniamahmood38
▴ 60
0
votes
2
replies
1.2k
views
Get fasta sequences with Biopython
sequence
genome
4.7 years ago by
florian.grosmaire
• 0
0
votes
0
replies
728
views
Feature Vector for drugs
drug
feature vector
ddi
neural network
4.7 years ago by
srijanibagchi
• 0
0
votes
1
reply
2.3k
views
AssertionError: not all umis are the same length(!): 4 - 5
umitools
RNA-Seq
umi
updated 4.7 years ago by
zx8754
12k • written 4.7 years ago by
monalisa6hota
• 0
0
votes
3
replies
920
views
Can you use high quallity annotation of very closely related to annotation novel genome
annotation
4.7 years ago by
robert.murphy
▴ 110
0
votes
1
reply
1.0k
views
Job:
Hiring: Bioinformatician at MiroBio, Oxford, UK
bioinformatician
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
m.jackson
• 0
0
votes
3
replies
2.3k
views
Creating HTO Count Matrix for Demultiplexing
single cell
cell hashing
cite seq
updated 4.7 years ago by
gildas.lepennetier
▴ 10 • written 4.8 years ago by
fouerghi20
▴ 90
0
votes
0
replies
989
views
Connection between Viterbi, Needleman Wunsch and Baum-Welch Algorithm
alignment
sequencing
viterbi
baum-welch
4.7 years ago by
trinityduke100
▴ 10
0
votes
3
replies
1.4k
views
best transformation for large RNAseq dataset
RNA-Seq
DESeq2
normalization
transformation
VST
4.7 years ago by
loipf
• 0
1
vote
2
replies
2.1k
views
How to download a list pdb codes contained in a csv file using
Biopython
updated 19 months ago by
Ram
45k • written 4.7 years ago by
jmungar2
▴ 10
0
votes
0
replies
1.9k
views
pathview graphviz plot problem.
pathview
kegg
4.7 years ago by
MatthewP
★ 1.4k
0
votes
1
reply
3.3k
views
get counts by gene for single cell rna seq
scRNA-seq
single-cell
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
das2000sidd
▴ 30
3
votes
14
replies
5.0k
views
Optimizing De Novo Transcriptome assemblies for non model organisms
Assembly
rna-seq
updated 3.6 years ago by
Ram
45k • written 10.7 years ago by
giorgiocasaburi
▴ 90
0
votes
1
reply
1.1k
views
SNPs id conversion from one database to another
SNP
genome
assembly
Genotyping
4.7 years ago by
tothepoint
▴ 940
0
votes
0
replies
943
views
Bowtie2 Alignment Summary vs Samtools
alignment
bowtie2
samtools
4.7 years ago by
ATRX
★ 1.2k
0
votes
4
replies
1.8k
views
MultiQC real threshold in every parameter
MultiQC
FastQC
RNA-Seq
quality control
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
jimmy0958073736
▴ 40
0
votes
2
replies
2.6k
views
use gatk phased vcf as input file of HapCut2
HapCut2
gatk
phasing
vcf
4.7 years ago by
Peter Chung
▴ 210
5
votes
4
replies
3.5k
views
renaming flow frames in a flowSet using flowCore
flow cytometry
R
flowCore
updated 4.7 years ago by
jaro.slamecka
▴ 270 • written 4.7 years ago by
imdoingascience
▴ 40
0
votes
0
replies
569
views
how to get the HBV infection information of the donors from ICGC database
gene
SNP
genome
sequence
assembly
updated 4.7 years ago by
Biostar
20 • written 4.8 years ago by
smallblue0402
• 0
0
votes
1
reply
948
views
I need to create a box plot for RPKM normalised data, can anyone please help me to make me understand, how to create a box plot for this given data
R
rna-seq
4.7 years ago by
rishav513
▴ 30
0
votes
0
replies
1.0k
views
Good practice for merging different sets of Plink data files
Plink
GWAS
4.7 years ago by
guessit
• 0
0
votes
1
reply
1.0k
views
Common SNPs (UCSC genome browser)
SNP
4.7 years ago by
sandsol97
• 0
4
votes
4
replies
1.8k
views
OMA standalone, parallelization
oma
parallelization
sge
qsub
updated 4.7 years ago by
Adrian Altenhoff
★ 1.1k • written 4.7 years ago by
mar.ark.parr
▴ 40
0
votes
3
replies
1.4k
views
Where can I find the raw data for this GSE entry?
GSE
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
pomodoro_sinensis
▴ 130
0
votes
1
reply
1.8k
views
How do I organize snakemake when not all jobs successfully output files from previous rule?
snakemake
workflow
python
4.7 years ago by
timothy.delory
▴ 20
0
votes
1
reply
1.5k
views
Need Insight into good courses/certifications to get as a bioinformatics scientist/computational biologist to boost resume & skills.
next-gen
genome
gene
sequencing
updated 4.7 years ago by
hh
• 0 • written 4.7 years ago by
screadore
▴ 20
0
votes
0
replies
1.0k
views
how to filter multi-KEGG_ko mapping after functional anntotion using eggnog-mapper
next-gen-sequencing
gene
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
MEITUO
▴ 10
0
votes
0
replies
5.8k
views
ValueError: Invalid file path or buffer object type: <class 'snakemake.io.Namedlist'>
Snakemake
4.7 years ago by
Kaya_Lena
• 0
3
votes
2
replies
1.6k
views
Cut&Tag / ChIPseq analysis
ChIP-Seq
Cut&tag
4.7 years ago by
wenbinm
▴ 40
0
votes
0
replies
839
views
Job:
Job Posting - Computational Biologist at UTSW
RNA-Seq
next-gen
ChIP-Seq
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
Laura.banaszynski
• 0
0
votes
0
replies
639
views
How to get coverage for specific base(s), and for specific mismatch(es) per genomic range
RNA-Seq
4.7 years ago by
lechu
▴ 20
1
vote
10
replies
3.5k
views
ERROR::: vcf to PLINK
PLINK
GWAS
VCFs
updated 4.7 years ago by
Sam
★ 4.8k • written 4.7 years ago by
Kumar
▴ 170
0
votes
3
replies
1.3k
views
strange looking bcftools norm file
bcftools
samtools
variant
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
hello_bioinf
▴ 250
4
votes
4
replies
1.4k
views
Identifying novel mRNA transcripts
RNA-Seq
updated 4.7 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
Pranathi
▴ 10
122,214 results • Page
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Comment: circos plot for genomic features
by
colindaven
8.1k
Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/ You can load both haplotypes, use minimap2 to create a paf …
Comment: How excactly is the Q30 is calculated?
by
colindaven
8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
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 …
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