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122,207 results • Page
690 of 2445
Sort: Rank
Rank
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Votes
Replies
1
vote
4
replies
2.9k
views
BLAST results shows partial matches
blast
BLAST
assembly
4.7 years ago by
langziv
▴ 70
10
votes
18
replies
4.9k
views
How to concatenate FASTA files in a specific order based on sequence ID
sequence
fasta
awk
python
pipeline
4.7 years ago by
Apex92
▴ 320
5
votes
4
replies
1.5k
views
Could I analyze just a few genes of a BAM file?
RNA-Seq
BAM
updated 4.5 years ago by
Ram
45k • written 4.7 years ago by
Zahra
▴ 110
1
vote
2
replies
1.4k
views
Some questions about the CPTAC data processing
programming
genomics
protein
4.6 years ago by
tujuchuanli
▴ 140
1
vote
1
reply
1.1k
views
Forum:
Sharing frequently asked questions about microbial genome sequencing II
microbial
faq
genome
sequencing
meta
updated 4.7 years ago by
Istvan Albert
103k • written 4.7 years ago by
Novogene
▴ 520
0
votes
2
replies
2.5k
views
Reactome Pathway Analysis from command line
RNA-Seq
gene
updated 4.7 years ago by
darklings
▴ 590 • written 7.8 years ago by
saamar.rajput
▴ 80
3
votes
4
replies
1.7k
views
Fasta header contain multiple string
fasta
updated 4.7 years ago by
cpad0112
21k • written 4.7 years ago by
harry
▴ 40
4
votes
3
replies
1.9k
views
K-mer usage in metagenome assemblies
Assembly
metagenomics
k-mer
4.7 years ago by
v.berriosfarias
▴ 140
4
votes
3
replies
4.3k
views
Downsampling fastq reads
next-gen
metagenomics
updated 4.7 years ago by
onestop_data
▴ 330 • written 4.8 years ago by
mario_de_manner
▴ 20
2
votes
4
replies
2.8k
views
featureCounts assignment low when mapping to "exon"
RNA-seq
E.coli
featureCounts
4.7 years ago by
gt
▴ 30
8
votes
0
replies
4.0k
views
Tutorial:
Pipes in R: An introduction and some advanced tips and tricks.
R
4.7 years ago by
rpolicastro
13k
0
votes
0
replies
848
views
NormFinder Error
Normalization
R-Studio
RNASeq
4.7 years ago by
far.zi
▴ 10
2
votes
4
replies
2.2k
views
How to calculate variant length for each sample
genome
updated 4.7 years ago by
Istvan Albert
103k • written 4.7 years ago by
lz1903
▴ 10
4
votes
3
replies
1.6k
views
Score from correlations per genes in DGE results
scoring
genomics
rna
enrichment
updated 4.7 years ago by
rpolicastro
13k • written 4.7 years ago by
Lopiniatre
▴ 10
74
votes
28
replies
21k
views
13 follow
Tool:
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq
SRA
updated 8 weeks ago by
Guilherme
• 0 • written 6.7 years ago by
Phil Ewels
★ 1.5k
2
votes
3
replies
1.7k
views
References saying that BWA is not quite specific
bwamem
aligner
4.7 years ago by
marongiu.luigi
▴ 770
0
votes
0
replies
1.1k
views
ChIP-seq peak calling with MACS2 - some large peaks for transcription factor
chip-seq
macs2
peakcalling
4.7 years ago by
becky.reese17
• 0
1
vote
3
replies
3.8k
views
ChromHMM: chromatin states to genome % coverage?
ChIP-Seq
ChromHMM
updated 4.7 years ago by
Yussuf
• 0 • written 8.7 years ago by
Sy80
▴ 10
3
votes
5
replies
5.2k
views
SingleR Cluster-wise annotation
Seurat
SingleR
annotation
scRNA-seq
CellType
updated 4.7 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
mvis1231
▴ 140
3
votes
2
replies
1.4k
views
find overlapping transcripts
transcript
RNAseq
updated 4.7 years ago by
Alex Reynolds
36k • written 4.7 years ago by
robinycfang
▴ 20
2
votes
2
replies
1.5k
views
How to split the .bigWig file into equal size of bin?
programming
mapping
alignment
updated 4.7 years ago by
Alex Reynolds
36k • written 4.7 years ago by
solarchan7
• 0
2
votes
7
replies
2.7k
views
PCAplot to investigate PC2 loadings using DESeq data
PCATools
4.7 years ago by
n.tear
▴ 80
3
votes
11
replies
3.2k
views
Important genes are not differentially expressed
genomics
R
DEseq2
Rnasequencing
updated 4.7 years ago by
Santosh Anand
5.8k • written 4.7 years ago by
bionewbie
• 0
0
votes
0
replies
1.4k
views
prepDE.py read length choice for paired-end sequencing reads
data
genomics
4.6 years ago by
1234gingko
▴ 50
2
votes
2
replies
1.3k
views
How to find that genes are up or down-regulated in which condition
enrichment
sequencing
python
genomics
4.7 years ago by
StartR
▴ 30
2
votes
2
replies
1.3k
views
Asking for papers: rare variants of potentially moderate impact
human
disease
genetics
4.7 years ago by
German.M.Demidov
★ 3.0k
6
votes
5
replies
2.1k
views
TB drug resistance pipeline
genomics
workflow
updated 4.0 years ago by
Jody Phelan
▴ 10 • written 4.7 years ago by
Moneeb Bajwa
▴ 10
3
votes
5
replies
3.2k
views
Hi-C: getting intervals from "A Compendium of Chromatin Contact Maps Reveal Spatially Active Regions in the Human Genome"
Hi-C
intervals
chromosome
interaction
tad
updated 6.9 years ago by
Devon Ryan
105k • written 6.9 years ago by
Pierre Lindenbaum
166k
0
votes
4
replies
4.5k
views
SRA tool kit 2.9.4
software error
updated 4.7 years ago by
GenoMax
154k • written 6.7 years ago by
mohsinazeem30
• 0
0
votes
0
replies
947
views
Job:
Single cell genomic approaches to study mitochondrial genetics and disorders
immunology
cellmulti-omics
mitochondrialgenetics
4.7 years ago by
info
▴ 30
0
votes
1
reply
1.5k
views
Job:
Carry out your own PhD project! - In Single Cell Genomics and Mitochondrial Genetics
PhD
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
info
▴ 30
0
votes
8
replies
2.3k
views
Upload data in tripal
database
tripal
4.5 years ago by
felipead66
▴ 120
0
votes
0
replies
1.1k
views
error when using ViSEAGO package
geneontology
ViSEAGO
4.7 years ago by
peter.berry5
▴ 60
0
votes
1
reply
939
views
Curate a specific Reference Database only containing species/strains belonging to one bacterial family
RStudio
microbiome
NGS
referencedatabase
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
Raphaela
▴ 10
0
votes
2
replies
1.6k
views
I use Mutects of Variant Call for paired Tumor/Normal WES, do I get a credibility (p value) for each call?
Mutect2
GATK
WES
Funcotator
4.6 years ago by
field654
▴ 30
0
votes
1
reply
1.6k
views
bcftools csq creates no output
genotyping
sequencing
dna
format
4.7 years ago by
ommegang
▴ 10
0
votes
0
replies
943
views
News:
3-day ONLINE TRAINING - NEXTFLOW
pipeline
programming
workflow
cloud
clustering
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
Physalia-courses
★ 2.7k
0
votes
0
replies
764
views
What is the best practice for gene tree - species tree reconcilation?
gene-tree
phylogenetics
species-tree
NOTUNG
4.7 years ago by
1099
• 0
1
vote
1
reply
1.3k
views
Calculate allele frequencies per population with SNPRelate
SNPRelate
allelefrequencies
plink
SNP
R
updated 4.7 years ago by
jena
▴ 330 • written 4.7 years ago by
irieljoerin
▴ 40
0
votes
0
replies
950
views
Job:
2 Postdoctoral fellows in Metabolic Engineering at DTU Biosustain
FACS
GC-MS
HPLC
LC-MS
4.7 years ago by
info
▴ 90
1
vote
1
reply
1.1k
views
Use of megSAP
general
updated 4.7 years ago by
German.M.Demidov
★ 3.0k • written 4.7 years ago by
tomtom.ziegler
• 0
0
votes
9
replies
3.3k
views
How to do the gene ontology analysis for the list of genes
R
RNAseq
geneontology
rna
goseq
updated 4.7 years ago by
Friederike
9.0k • written 4.7 years ago by
luckysardar171
▴ 20
1
vote
7
replies
3.7k
views
Cutadapt or Trim Galore for SMART-seq?
TrimGalore
galaxy
SmartSeq
rna
Cutadapt
4.7 years ago by
Youyy
• 0
6
votes
6
replies
2.5k
views
plain list of human cell lines
human cell lines
4.7 years ago by
bstrs
• 0
1
vote
1
reply
958
views
Reasons for drops in alignment
alignment
quality
updated 4.7 years ago by
German.M.Demidov
★ 3.0k • written 4.7 years ago by
marongiu.luigi
▴ 770
2
votes
3
replies
2.4k
views
Only a small portion of my reads have Smart-seq adapters, why?
Smartseq
RNAseq
rna
galaxy
illumina
4.7 years ago by
Youyy
• 0
0
votes
0
replies
807
views
Difference between Whole Exome Sequencing Pipeline for IonTorrent and Illumina?
pipeline
ngs
whole-exome-sequencing
updated 4.7 years ago by
ATpoint
90k • written 4.7 years ago by
NikhilP
▴ 20
7
votes
2
replies
26k
views
GRCm39 (mm39) vs GRCm38(mm10)
genome
reference
mouse
DNA
dna
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
askif4
▴ 20
0
votes
5
replies
2.4k
views
mapping unavailable in Blast2GO
mapping
blast
updated 4.7 years ago by
lieven.sterck
16k • written 4.7 years ago by
hugo.denis
• 0
0
votes
1
reply
1.5k
views
Distance Matrix Calculation
genome
biopython
updated 4.7 years ago by
gb
★ 2.2k • written 4.7 years ago by
anasjamshed
▴ 140
122,207 results • Page
690 of 2445
Recent Votes
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
Trimming sequences based on NCBI contamination screen report
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Biomed-jeh
▴ 70
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Recent Replies
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…
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…
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