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122,216 results • Page
715 of 2445
Sort: Rank
Rank
Views
Votes
Replies
1
vote
0
replies
3.6k
views
Functional annotation(GO,KEGG): Blast2GO+KAAS or EggNOG
blast2go
eggnog
kegg
rna-seq
genome
updated 4.8 years ago by
Biostar
20 • written 5.6 years ago by
tianshenbio
▴ 190
0
votes
8
replies
1.9k
views
Bacterial RNA-SEQ - Quality Control
RNA-Seq
updated 4.8 years ago by
swbarnes2
15k • written 4.8 years ago by
Sammy
▴ 30
0
votes
5
replies
2.5k
views
umi_tools using regex greedy quantifiers only returning 1 character
regex
umi_tools
updated 2.5 years ago by
Ram
45k • written 4.8 years ago by
williamtmills
▴ 20
0
votes
4
replies
2.3k
views
Where can I find data about gene expression in such diseases as bipolar (maniacal/depressive phases), depression, paranoia?
gene
expression
desease
database
updated 4.8 years ago by
seidel
11k • written 4.8 years ago by
philosophical.raptor111
• 0
2
votes
13
replies
2.5k
views
complexheatMap runtime error
Complexheatmap
R
updated 4.8 years ago by
Biostar
20 • written 4.9 years ago by
amitpande74
▴ 20
6
votes
11
replies
2.1k
views
Recommendations for genome-wide genotyping platform, array and data analysis software?
genotyping
4.8 years ago by
anamaria
▴ 220
7
votes
7
replies
6.7k
views
RNA-seq ribosomal genes vs proteins
RNA-Seq
scRNA-seq
rRNA
updated 4.8 years ago by
predeus
★ 2.1k • written 4.8 years ago by
igor
13k
6
votes
5
replies
2.3k
views
Kept getting issue when using ImmGenData() in SingleR
R
SingleR
4.8 years ago by
leranwangcs
▴ 150
2
votes
3
replies
1.4k
views
Combine two independent Seurat analysis into a single one
RNA-Seq
seurat
updated 4.8 years ago by
Ram
45k • written 4.8 years ago by
elb
▴ 260
2
votes
1
reply
3.3k
views
Interpreting ATAC-SEQ motif enrichment output
ATAC-Seq
ChIP-Seq
updated 4.8 years ago by
ATpoint
90k • written 4.8 years ago by
emalekos
▴ 40
5
votes
5
replies
2.9k
views
How to select a "representative" transcript in multiple transcript variants from annotation with ANNOVAR and gencode
annovar
gencode
transcript
SNP
annotation
4.8 years ago by
svlachavas
▴ 790
1
vote
3
replies
1.4k
views
Retrieve unique human membrane protein coding genes in Uniprot
Uniprot
membrane proteins
human genome
updated 4.8 years ago by
Elisabeth Gasteiger
★ 2.4k • written 4.8 years ago by
PRog
▴ 10
1
vote
6
replies
2.7k
views
Problems removing specific contig from .bam file
samtools
WGS
bam
genome
picard
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
USA_225478
• 0
0
votes
3
replies
1.4k
views
Bacterial (E.coli) RNA-SEQ differential gene expression (with pET system)
rna-seq
updated 4.8 years ago by
Joe
22k • written 4.8 years ago by
Sammy
▴ 30
5
votes
1
reply
1.7k
views
News:
Paid opportunity: need microbiome experts for a survey and test of robustness
survey
updated 2.8 years ago by
Ram
45k • written 5.1 years ago by
Jeremy Leipzig
23k
0
votes
1
reply
1.5k
views
News:
The NCBI Datasets command-line tool now provides ortholog data
ncbi
gene
json
refseq
updated 2.8 years ago by
Ram
45k • written 4.8 years ago by
e.cox
▴ 50
13
votes
3
replies
7.2k
views
Forum:
Can We Have A Collection Of Interesting Research Topics?
project
phd
updated 2.8 years ago by
Ram
45k • written 13.5 years ago by
Michael
56k
3
votes
1
reply
4.8k
views
Three way comparison RNAseq libraries
RNA-Seq
R
Analysis
updated 2.9 years ago by
Ram
45k • written 10.5 years ago by
rodrigo.nicodemos82
▴ 10
0
votes
6
replies
2.4k
views
What are the best quantification tools for miRNA seq?
miRNA
RNA-Seq
Salmon
miRNA-seq
4.8 years ago by
cecilomar6
• 0
3
votes
2
replies
976
views
What dataset do I use to annotate a transcriptome? Another transcriptome or a genome?
alignment
RNA-Seq
updated 3.9 years ago by
lieven.sterck
16k • written 4.8 years ago by
pseudacris
▴ 10
1
vote
4
replies
1.3k
views
How to convert the position of probes into Gene symbol or Entrez_id(Platform GPL16110)
geo
updated 2.4 years ago by
Ram
45k • written 4.8 years ago by
linhzye
▴ 10
0
votes
1
reply
1.1k
views
Breast cancer expression data with subtype information
breast cancer
data
subtype
expression
dataset
4.8 years ago by
sabin
▴ 50
0
votes
0
replies
641
views
How can I convert the transcript coordinate to a genomic coordinate?
RNA-Seq
Assembly
sequence
4.8 years ago by
qwesxadzc9
• 0
0
votes
5
replies
2.1k
views
Mapping a short primer sequence to a whole genome
alignment
updated 4.8 years ago by
shenwei356
8.7k • written 4.8 years ago by
robert.murphy
▴ 110
5
votes
6
replies
2.1k
views
How to install R in WinSCP server
R
updated 4.8 years ago by
Shred
★ 1.6k • written 4.8 years ago by
Fede_Santos95
▴ 20
2
votes
1
reply
2.2k
views
What are the best scATAC-seq computational pipelines / tools / literature currently available?
single-cell
scATAC-seq
ATAC-seq
pipeline
4.8 years ago by
Sergio Martínez Cuesta
▴ 230
2
votes
4
replies
1.9k
views
Finding Fragment Size chip-seq paired end reads
ChIP-Seq
sequencing
4.8 years ago by
luckysardar171
▴ 20
1
vote
0
replies
2.6k
views
fitting model to a read coverage spectra
genome
k-mer spectra
read coverage
updated 4.8 years ago by
Biostar
20 • written 8.6 years ago by
Damian Kao
16k
0
votes
0
replies
1.7k
views
Tool:
I made QMplot: a python library and tools of generating high-quality manhattan and Q-Q plots for GWAS data
visualization
Manhattan-Plot
GWAS
genome
Python
updated 2.5 years ago by
Ram
45k • written 4.8 years ago by
huangshujia9
• 0
2
votes
1
reply
1.0k
views
module vs miniconda in HPC
module
miniconda
conda
HPC
4.8 years ago by
Friyunnwoo
▴ 20
0
votes
3
replies
1.0k
views
Fisher exact test for 2 by 20000 table and for 4 by 20000 table
gene
4.8 years ago by
Rob
▴ 180
2
votes
1
reply
1.1k
views
bcftools command not working
bcftools
dna-seq
SNP
updated 4.8 years ago by
GenoMax
154k • written 4.8 years ago by
gt
▴ 30
4
votes
4
replies
4.8k
views
How do I use FindAllMarkers after making additional cluster assignments?
Seurat
R
single cell-RNA seq
scRNA-seq
4.8 years ago by
Pratik
★ 1.1k
1
vote
1
reply
1.2k
views
FastQC per base to total base calculator
FastQC
MultiQC
GC%
N-content
4.8 years ago by
jimmy0958073736
▴ 40
2
votes
4
replies
3.9k
views
Pharmgkb: Obtain A List Of Vip Genes And List All Linked Drugs To Them
pharmgkb
updated 4.8 years ago by
Ram
45k • written 13.7 years ago by
User56
▴ 100
0
votes
1
reply
729
views
Downloading multiple studies SRA data through while loop
e-utilities
4.8 years ago by
jobrien20
• 0
0
votes
2
replies
776
views
finding bacterial genes in dataset
microbiome
gene
sequencing
4.8 years ago by
john.chandler2011
• 0
0
votes
0
replies
932
views
Cluster Stability Assesment
rna-seq
Seurat
clustering
R
4.8 years ago by
Maria17
▴ 40
0
votes
4
replies
1.4k
views
Bacterial refseq to remove contaminats
transcritpome
RNA-seq
updated 4.8 years ago by
gamamiguelangel
• 0 • written 4.8 years ago by
Rogerio Ribeiro
▴ 110
1
vote
5
replies
2.6k
views
SRA toolkit fastq files download error
RNA-Seq
SRA
4.8 years ago by
sidrah.maryam
▴ 70
0
votes
0
replies
979
views
kallisto preprocessing-Error: unspliced. bus has no BUS records
kallisto
RNA-Seq
bustools
updated 2.5 years ago by
Ram
45k • written 4.8 years ago by
gabriella.wangyi1986
• 0
0
votes
3
replies
1.2k
views
Very small quantity of adapter contamination, real or not?
next-gen
DNA-seq
Quality control
Adapters
4.8 years ago by
Ismaelrymy
• 0
0
votes
2
replies
2.0k
views
Extract unmapped sequenced from a sam file output from minimap2
get unmapped reads from sam file
updated 4.8 years ago by
JC
13k • written 4.8 years ago by
ja569116
• 0
4
votes
2
replies
1.8k
views
Help with Mr Bayes parameters for 16S phylogeny
sequence
Assembly
mrbayes
4.8 years ago by
buhbs
▴ 30
0
votes
5
replies
3.3k
views
Multi-factor time series design model in DESeq2 analysis
RNA-Seq
updated 3.1 years ago by
Ram
45k • written 10.3 years ago by
prppmet
• 0
2
votes
3
replies
2.0k
views
Short sequence alignment using Minimap2
assembly
minimap2
kmer
gRNA
pacbio
updated 4.6 years ago by
GenoMax
154k • written 4.8 years ago by
Sbrillo
▴ 10
2
votes
1
reply
827
views
Collapse bed and only sum overlapping parts
bed
RNA-Seq
alignment
4.8 years ago by
Matthias
▴ 30
1
vote
1
reply
726
views
Rna-seq time series dataset
RNA-Seq
next-gen
updated 4.8 years ago by
GenoMax
154k • written 4.8 years ago by
roberta.orru095
• 0
8
votes
10
replies
2.4k
views
Forward and reverse single cell data analysis
RNA-Seq
updated 4.8 years ago by
swbarnes2
15k • written 4.8 years ago by
elb
▴ 260
3
votes
9
replies
5.9k
views
6 follow
Multiple ensembl gene ID for the same gene name (Symbol), how to deal with this while differential analysis?
RNA-Seq
alignment
next-gen
ensembl
updated 3.6 years ago by
ccfpwll
▴ 10 • written 4.8 years ago by
Swarna Kanchan
▴ 10
122,216 results • Page
715 of 2445
Recent Votes
Comment: circos plot for genomic features
Answer: How to perform GO enrichment in non-model organisms?
Comment: circos plot for genomic features
Answer: How excactly is the Q30 is calculated?
A: PCA in a RNA seq analysis
what cause poly-G from NextSeq
what cause poly-G from NextSeq
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Recent Replies
Comment: Question about QC and scrublet
by
Arup Ghosh
3.5k
You can run Scrublet before filtering cells with high gene counts and compare the doublet score vs `n_counts_genes`.
Answer: How to perform GO enrichment in non-model organisms?
by
lieven.sterck
16k
In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed. …
Comment: circos plot for genomic features
by
Matteo Ungaro
▴ 140
@colindaven thanks a lot! `clinker` also seems to be a nice/effective tool to do so. It happens we stuble across a work where they used `Ci…
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
▴ 140
@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…
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