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122,212 results • Page
703 of 2445
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0
votes
0
replies
746
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Is it possible to do an analysis of rna-seq of specific data from dataset or should I do the whole dataset?
RNA-Seq
sequence
next-gen
4.7 years ago by
ashwing.kofficial
▴ 10
1
vote
1
reply
11k
views
Negative normalized Enrichment Score (NES) in GSEA analysis
GSEA
updated 3.3 years ago by
Ram
45k • written 10.0 years ago by
Phil S.
▴ 700
6
votes
10
replies
3.8k
views
Removing chrEBV reads from bam file
bam
genome
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
Marco Pannone
▴ 810
3
votes
5
replies
5.3k
views
Problems with ArrayExpress datasets downloads on Bioconductor
arrayExpress
bioconductor
updated 4.7 years ago by
Hannes
▴ 60 • written 6.8 years ago by
Davide Chicco
▴ 120
0
votes
0
replies
934
views
News:
Learn how to do modern reproducible data science
Snakemake
Workflows
Nextflow
updated 2.8 years ago by
Ram
45k • written 4.7 years ago by
Physalia-courses
★ 2.7k
0
votes
2
replies
3.2k
views
Variant calling 10x 3' scRNA data?
10x
rna-seq
RNA-Seq
snp
4.7 years ago by
scrnaresearch
▴ 10
0
votes
5
replies
2.0k
views
How to calculate p-values from PLINK output by hand
plink
p-values
4.7 years ago by
L_to_the_m
▴ 10
8
votes
9
replies
3.7k
views
BLASTP - HSPs and bitscores
BLASTP
hsp
bit-score
updated 4.7 years ago by
lieven.sterck
16k • written 4.7 years ago by
timothy.kirkwood
▴ 140
0
votes
0
replies
891
views
News:
Noncoding RNA conference (including bioinformatics)
conference
RNA
noncoding-RNA
updated 2.8 years ago by
Ram
45k • written 4.7 years ago by
rory.johnson
▴ 20
7
votes
19
replies
5.0k
views
DNA sequence complexity with a sliding window
R
python
dna
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
User000
▴ 750
0
votes
1
reply
1.3k
views
Instrumental Variables and confounder in Mendelian Randomization
Variables
Mendelian
randomization
Instrumental
4.6 years ago by
Shicheng Guo
★ 9.6k
1
vote
1
reply
1.7k
views
Is there any problem on Mendelian Randomization analysis with binary exposure and outcome?
SNP
updated 4.7 years ago by
Amy Mason
• 0 • written 7.2 years ago by
sjunlee89
▴ 10
2
votes
4
replies
3.3k
views
[OP Inactive] clusterProfiler (enrichKEGG) error
kegg
clusterProfiler
Guangchuang Yu
updated 4.7 years ago by
Biostar
20 • written 7.6 years ago by
bikash2510
▴ 30
4
votes
6
replies
2.2k
views
Weird MAplot with DEGs lying along the diagonals
microarray
maplot
normalization
agilent
updated 4.7 years ago by
rpolicastro
13k • written 4.7 years ago by
FedeXandeR
▴ 20
0
votes
2
replies
1.8k
views
Searching for a free alternative to IPA
rna-seq
ipa
4.7 years ago by
francesca3
▴ 160
0
votes
2
replies
1.4k
views
freebayes calls presumably homozygous variants as heterozygotes
SNP
freebayes
variant-call
genotyping
updated 20 months ago by
virginia.baraja
• 0 • written 4.7 years ago by
johanna.pieplow
• 0
1
vote
3
replies
1.6k
views
Mapping reads to contigs with BBMap - output statistics question (metagenome)
Assembly
alignment
Metagenome
4.7 years ago by
bioknown
• 0
0
votes
0
replies
702
views
How to select parameters for RNAplfold?
RNA-Seq
rna-seq
sequence
4.7 years ago by
qwesxadzc9
• 0
1
vote
0
replies
887
views
Measuring Co-Occurrence of Gene Clusters (Bacteria)
antismash
gene clusters
co-occurrence
4.7 years ago by
biohacker_tobe
▴ 80
4
votes
13
replies
5.3k
views
Creating a Contingency Table (Gene Absence Presence)
gene
R
microbes
dataframe
genome
4.7 years ago by
biohacker_tobe
▴ 80
0
votes
0
replies
1.3k
views
Co-Occurrence Heatmap Creation
ggplot2
r
R
heatmap
statistics
4.7 years ago by
biohacker_tobe
▴ 80
6
votes
3
replies
8.1k
views
Co-Occurrence Network Graph & Statistics
R
networks
dataframe
4.7 years ago by
biohacker_tobe
▴ 80
6
votes
3
replies
5.9k
views
Run R in multi threaded
R
updated 4.7 years ago by
Kevin Blighe
★ 90k • written 9.8 years ago by
win
▴ 990
0
votes
0
replies
675
views
need advice for comparing fragment counts of genes across multiple WGS metagenomes
WGS
normalization
KMA
4.7 years ago by
sapuizait
▴ 10
0
votes
0
replies
895
views
Forum:
Tools to check if the user defined pathway is enriched in the data
RNA-Seq
sequencing
R
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
Aynur
▴ 60
1
vote
1
reply
2.3k
views
Why is my miRNA-seq mapping rate so low?
sequencing
miRNA
miRNA-seq
RNA-Seq
4.7 years ago by
cecilomar6
• 0
1
vote
3
replies
1.2k
views
How to include NCBI blastp while making an online database?
python
database
NCBI
updated 4.7 years ago by
Carambakaracho
★ 3.3k • written 4.7 years ago by
ThulasiS
▴ 90
0
votes
3
replies
1.0k
views
LeuceGene AML data Survival, Clinical and Mutation Data
RNA-Seq
AML
4.7 years ago by
onkarmulay10
• 0
0
votes
0
replies
909
views
tophat2 mapping fr-firststrand or fr-secondstrand ?
tophat2
fr-firststrand
fr-secondstrand
AB SOLiD
4.7 years ago by
debitboro
▴ 270
1
vote
3
replies
1.6k
views
What file to use for Deseq2 and where to get it from
RNA-Seq
sequencing
next-gen
updated 4.7 years ago by
ATpoint
90k • written 4.7 years ago by
ashwing.kofficial
▴ 10
0
votes
0
replies
871
views
DAVID Bioinformatics tool
David
data visulization
4.7 years ago by
joyeeta.dutta.in
• 0
0
votes
2
replies
883
views
Error in platanus: file format exception
assembly
4.7 years ago by
yamkelamgwatyu
• 0
1
vote
3
replies
2.5k
views
Can we compare peaks of different transcription factors when they were obtained by different criteria (IDR/FDR)?
ChIP-Seq
IDR
RNA-Seq
updated 4.7 years ago by
Biostar
20 • written 7.3 years ago by
salamandra
▴ 550
0
votes
2
replies
1.6k
views
KOBAS 3.0 web server is down
KOBAS
updated 4.5 years ago by
bioadept
• 0 • written 4.7 years ago by
956120746
• 0
2
votes
7
replies
1.9k
views
dual-RNA seq combined reference alignment
RNA-Seq
updated 4.7 years ago by
sontiroy
• 0 • written 5.6 years ago by
u3005992
▴ 20
1
vote
5
replies
2.4k
views
what are the best metagenome assemblers?
assembly
updated 4.7 years ago by
956120746
• 0 • written 5.2 years ago by
Rubemsilva32
• 0
2
votes
2
replies
5.4k
views
Genome repeat masking before gene annotation
genome-annotation
updated 2.7 years ago by
Ram
45k • written 8.2 years ago by
abhijit.synl
▴ 60
0
votes
1
reply
987
views
[WGS] how to correctly visualize long indels (50nt+)
wgs
indel
visualization
igv
gatk
4.7 years ago by
memento1984_1
• 0
0
votes
1
reply
921
views
How to retrieve representative at 30% sequence identity in PDB
PDB
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
bosimiya
• 0
0
votes
0
replies
681
views
concatenate the human genome fasta file with the SARS-COV2 virus
RNA-Seq
genome
assembly
4.7 years ago by
FarnazTabrizi95
• 0
0
votes
3
replies
1.5k
views
Functional annotation of DESeq2 results?
RNA-Seq
rna-seq
gene
R
4.6 years ago by
snow4964
▴ 10
0
votes
0
replies
1.8k
views
Job:
Exciting Bioinformatician/Statistician Opportunity at Gladstone Insitutes (San Francisco)
RNA-Seq
genome
R
sequencing
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
janine.doerner
▴ 20
0
votes
0
replies
822
views
Can I use a subset of VCF my files for quality checks?
quality checks
relatedness
vcf
updated 4.7 years ago by
Biostar
20 • written 4.9 years ago by
floortje
• 0
2
votes
1
reply
1.1k
views
Prepare a GenBank submission: Can you turn this Perl script into a one-liner?
assembly
perl
code-golf
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
Michael
56k
2
votes
3
replies
3.9k
views
Making plots for enrichment and KEGG results
R
gene
updated 4.7 years ago by
halo22
▴ 300 • written 4.7 years ago by
ymervenuryavuz
• 0
0
votes
2
replies
1.1k
views
Linear regression on genotype data
SNP
updated 4.7 years ago by
halo22
▴ 300 • written 4.7 years ago by
khatami.mahshid
▴ 30
2
votes
2
replies
2.1k
views
clusterProfiler Results not showing
clusterprofiler
RNA-Seq
R
enrichKEGG
updated 4.7 years ago by
halo22
▴ 300 • written 4.7 years ago by
geoffkerr22
▴ 10
0
votes
0
replies
962
views
Using InterProScan - ATPase results only
sequence
InterProScan
annotation
4.7 years ago by
damt09
• 0
0
votes
0
replies
777
views
Why do my polysome and monosome-RNAs map to less exons?
RNA-Seq
sequencing
alignment
next-gen
Assembly
4.7 years ago by
joetaylor268
▴ 20
0
votes
0
replies
847
views
Variant Calling when Genetic Distance between Reference and Samples is Greater than it is for Humans: Does GATK still perform well?
GATK
variant calling
MASH
4.7 years ago by
robertwhbaldwin
• 0
122,212 results • Page
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How to trim transcripts using information from NCBI contamination screen report
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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.
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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
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▴ 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…
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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…
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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…
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