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122,202 results • Page
686 of 2445
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0
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715
views
how to build a graph reference with HISAT-genotype
reference
RNA-seq
hisat2
alignment
4.6 years ago by
minghuiguo448
• 0
2
votes
2
replies
1.4k
views
Convert protein name to letter e.g. p.Arg135Trp to p.R135W
aminoacid
updated 4.6 years ago by
cpad0112
21k • written 4.6 years ago by
whb
▴ 60
0
votes
0
replies
1.5k
views
Will there be late amplification (ct value) for negative control in qPCR?
RNA
QPCR
cDNA
4.6 years ago by
shail.nair05
▴ 20
3
votes
7
replies
2.5k
views
7 follow
Annotation of non model fish (mahi mahi) genome
Assembly
Annotation
updated 4.6 years ago by
Juke34
9.3k • written 5.4 years ago by
kspata
▴ 90
2
votes
1
reply
1.3k
views
Building a biological database of coding sequence of Covid-19 with Python
python
covid
project
database
covid-19
updated 4.6 years ago by
tothepoint
▴ 940 • written 4.6 years ago by
aziznasr1920
▴ 10
1
vote
1
reply
1.1k
views
Argument "query". Incompatible with argument: `in_pssm' blast+
psiblast
ncbi
tblastn
blast
4.6 years ago by
rachid.fermi
• 0
3
votes
2
replies
1.3k
views
What does BP stand for? | Reads and Assemblies
Macrogenomics
read
assembly
updated 2.7 years ago by
Ram
45k • written 4.6 years ago by
Anonymous
▴ 10
1
vote
3
replies
2.0k
views
"MethylKit" package for WGBS data
subjective
updated 4.6 years ago by
Papyrus
★ 3.1k • written 4.7 years ago by
shrinka.genetics
▴ 40
1
vote
1
reply
1.0k
views
gemBS aligner file format
gemBS
aligner
updated 4.6 years ago by
GenoMax
154k • written 4.6 years ago by
shrinka.genetics
▴ 40
0
votes
2
replies
1.3k
views
Samtools view error: header include @SQ line missing LN tag.
minimap2
updated 2.7 years ago by
Ram
45k • written 4.6 years ago by
Digimon
• 0
3
votes
1
reply
1.6k
views
Calling TE sequences from VCF files
next-gen
variant-calling
sniffles
updated 2.1 years ago by
Ram
45k • written 6.0 years ago by
elcortegano
▴ 210
1
vote
2
replies
1.4k
views
How to choose the best alignment from mapping with bowtie2?
alignment
bowtie2
sequence
4.6 years ago by
anikcropscience
▴ 270
20
votes
8
replies
2.8k
views
9 follow
Forum:
What are some major historic shifts in bioinformatic methodologies?
meta
history
updated 4.6 years ago by
dariober
15k • written 4.7 years ago by
Jeremy Leipzig
23k
0
votes
0
replies
634
views
Experimental/Biological datasets for Gene Regulatory Network Reconstruction
Gene
network
data
Regulatory
microarray
Network
4.6 years ago by
Anjali Setiya
• 0
2
votes
4
replies
3.6k
views
Where can I find a fasta for mitochondrial genes?
mitochondrial
genes
updated 4.6 years ago by
Jorge Amigo
14k • written 4.7 years ago by
blur
▴ 280
0
votes
1
reply
1.4k
views
Where to download raw counts (RNAseq) and breakpoints coordinates (cancer related) for testing?
RNAseq
cancer
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
Lila M
★ 1.3k
2
votes
2
replies
2.4k
views
Interpretation of functional prediction pathogenicity scores regarding variants with multiple transcripts in ANNOVAR
annovar
pathogenicity
cancer
CADD
4.6 years ago by
svlachavas
▴ 790
4
votes
2
replies
1.7k
views
SNP‐based enrichment analysis for WGCNA modules using an hypergeometric test
hypergeometrictest
SNPs
WGCNA
4.6 years ago by
andres.firrincieli
3.9k
2
votes
5
replies
2.9k
views
MUtect2-Vardict
Mutect2
VarDict
NGS
updated 4.6 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
sarastrafella.ss
▴ 20
2
votes
2
replies
1.9k
views
featureCounts outputs zero raw read counts!!
featureCounts
DGE
updated 4.6 years ago by
GenoMax
154k • written 4.7 years ago by
kuntalasb
▴ 10
1
vote
4
replies
2.2k
views
CNA figure
python
figure
plot
R
CNA
updated 4.6 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
ehruan
▴ 10
0
votes
3
replies
1.4k
views
Genome assembly
assemblies
Genome
updated 4.6 years ago by
GenoMax
154k • written 4.7 years ago by
netipandey.87
▴ 10
2
votes
1
reply
2.3k
views
draw and display a Venn diagram with up to 7 sets.
Venn
updated 4.7 years ago by
Asaf
10k • written 4.7 years ago by
somayeh bakhshalizadeh
▴ 80
0
votes
0
replies
925
views
Job:
Postdoc position in non-coding RNA biology and bioinformatics
lncRNA
miRNA
Postdoc
RNA
updated 4.4 years ago by
Ram
45k • written 4.7 years ago by
heart.lncrna
• 0
0
votes
0
replies
1.0k
views
Pathway enrichment analysis vs GSEA for single cell RNA sequencing data analysis
GSEA
pathway
scRNAseq
4.7 years ago by
aa123
• 0
0
votes
1
reply
935
views
Patient-derived omics data with psychiatric illness scores like PANSS score
mentalillness
omicsdata
score
updated 4.6 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
sakuRa
• 0
4
votes
3
replies
6.5k
views
Getting all gene members in a Reactome Pathway
Reactome
Bioconductor
updated 4.7 years ago by
darklings
▴ 590 • written 6.3 years ago by
The
▴ 180
0
votes
1
reply
1.5k
views
Reactome reaction enumeration with DefinedSets
reactome
updated 4.7 years ago by
darklings
▴ 590 • written 6.1 years ago by
william.s.hayes
▴ 10
1
vote
2
replies
2.4k
views
Why is mapper.pl from mirdeep2 producing an empty mapping file?
mirna
ngs
next-gen
updated 4.7 years ago by
Yuquan
▴ 10 • written 5.0 years ago by
halo22
▴ 300
0
votes
2
replies
1.6k
views
Replace Drugbank IDs with Drug name [R]
r
dictionary
drugbank
updated 4.7 years ago by
rpolicastro
13k • written 4.7 years ago by
arissaoulidis
• 0
10
votes
15
replies
6.8k
views
conda install -c bioconda simlord | SimLoRD
ubuntu
bash
SimLoRD
reads
fastq
4.6 years ago by
Anonymous
▴ 10
0
votes
3
replies
10.0k
views
R: exporting summary of coxph object
R
Cox regression
data export
updated 4.7 years ago by
dwinsemius
• 0 • written 9.3 years ago by
orzech_mag
▴ 230
8
votes
3
replies
4.1k
views
Create duplicate columns in R for a large data frame
R
dataframe
updated 4.7 years ago by
cpad0112
21k • written 4.7 years ago by
Inquisitive8995
▴ 280
2
votes
2
replies
1.9k
views
TCGABioLinks getManifest() function. How to alter saved file name?
TCGA
R
Bioconductor
updated 4.7 years ago by
Jn Rmro
▴ 10 • written 4.9 years ago by
ivykosater
• 0
2
votes
6
replies
2.4k
views
A mismatch between DiffBind's results and the same results retreieved as DESeq2 (from DiffBind)
DiffBind
updated 4.6 years ago by
jared.andrews07
★ 19k • written 4.7 years ago by
Aspire
▴ 390
7
votes
3
replies
2.2k
views
Unable to match Ensembl IDs from TCGA-related CNV datasets
Ensembl
Number
TCGA
TCGABiolinks
Variation
Copy
updated 4.6 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
dc37
▴ 20
1
vote
1
reply
1.0k
views
How to find the taxonomic position of E.coli
ecoli
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
sutokska20
• 0
1
vote
4
replies
1.8k
views
How to select the reads with a certain adapter in a fastq file in R
SmartSeq
R
Bioconductor
Shortre
RNAseq
updated 4.7 years ago by
ATpoint
90k • written 4.7 years ago by
Youyy
• 0
0
votes
0
replies
1.2k
views
AXT format
sequence
alignment
multiple
mafft
4.7 years ago by
Rahul
▴ 30
0
votes
4
replies
2.3k
views
Replace headers of fasta while with simplified headers from another file
python
fasta
bash
updated 4.7 years ago by
cpad0112
21k • written 4.7 years ago by
Ava
• 0
0
votes
1
reply
1.5k
views
Blast a CDD PSSM against a genome
pssm
CDD
blast
updated 4.7 years ago by
Mensur Dlakic
★ 30k • written 4.7 years ago by
rubic
▴ 270
0
votes
1
reply
1.0k
views
Can the odds ratio change based on a multiple logistic regression model?
statistics
updated 4.7 years ago by
rpolicastro
13k • written 4.7 years ago by
Bioman
• 0
0
votes
1
reply
1.9k
views
Seurat: Any way to identify genes expressed only in one condition of one cluster?
scRNAseq
Seurat
updated 4.7 years ago by
jared.andrews07
★ 19k • written 4.7 years ago by
zhouyichaosdu
• 0
1
vote
10
replies
4.0k
views
Trimming customed adaptor sequences with trimmomatic
trimmomatic
trim
illumina
exon
updated 4.4 years ago by
Ram
45k • written 4.7 years ago by
1215045934
▴ 80
9
votes
11
replies
5.0k
views
Bash loop for bbduk
bash
bbduk
updated 4.7 years ago by
cpad0112
21k • written 4.7 years ago by
avelarbio46
▴ 30
0
votes
0
replies
1.2k
views
HybPiper Error
HybPiper
phylogeny
updated 3.0 years ago by
Ram
45k • written 4.7 years ago by
1215045934
▴ 80
3
votes
4
replies
4.3k
views
PRS using PGS Catalog
PRS
PGS
polygenic
PRSice
updated 4.2 years ago by
Sam
★ 4.8k • written 4.7 years ago by
Humza
▴ 10
0
votes
1
reply
1.6k
views
How to convert an RDS file containing annotated cells to a loom file
R
Scanpy
RNA-seq
updated 4.7 years ago by
rpolicastro
13k • written 4.7 years ago by
Olalekan
• 0
0
votes
3
replies
2.0k
views
Use of ISCN in public knowledgebases
sequence
updated 4.7 years ago by
Jng
• 0 • written 8.5 years ago by
bdolin
▴ 100
4
votes
4
replies
1.4k
views
How to get started with transcriptome sequencing as a bioinformatics beginner.
transcriptome
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
mariam28071993
• 0
122,202 results • Page
686 of 2445
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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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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 !
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
▴ 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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