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189 results • Page
2 of 4
Sort: replies
Rank
Views
Votes
Replies
3
votes
4
replies
318
views
Truncated metadata file report from ENA Portal API
ena
python
6 days ago by
Giulia
• 0
1
vote
4
replies
340
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 2 days ago by
Juke34
8.6k • written 3 days ago by
Vijith
▴ 30
1
vote
4
replies
339
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 3 days ago by
Ram
43k • written 8 days ago by
samRayne
• 0
1
vote
4
replies
289
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
12 hours ago by
diqixiaoyaoer
▴ 10
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 5 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
3
votes
4
replies
238
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
genome
updated 14 hours ago by
Ram
43k • written 21 hours ago by
Ali
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 2 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
0
votes
4
replies
300
views
Correlation Analysis
statistics
methylation
NGS
expression
5 days ago by
Researcher
▴ 30
0
votes
4
replies
242
views
calculating genomic coverage/ base overlap in R
genomics
updated 14 hours ago by
Ram
43k • written 1 day ago by
Xbox_27
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 3 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
0
votes
3
replies
160
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
1 day ago by
Esraa
• 0
3
votes
3
replies
280
views
what is another word for a BLAST "hit"?
blast
alignment
6 days ago by
dec986
▴ 380
1
vote
3
replies
790
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 10 hours ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
3
votes
3
replies
158
views
getting exon coordinates
genomics
updated 14 hours ago by
Ram
43k • written 15 hours ago by
Xbox_27
• 0
3
votes
3
replies
357
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 3 days ago by
Mathew
▴ 140 • written 6 days ago by
Christopher
• 0
0
votes
3
replies
203
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 6 hours ago by
Ram
43k • written 1 day ago by
vk
▴ 10
1
vote
3
replies
431
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
3 days ago by
kalavattam
▴ 190
1
vote
3
replies
283
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 6 days ago by
Ram
43k • written 6 days ago by
Omics data mining
▴ 260
0
votes
3
replies
352
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
3 days ago by
mropri
▴ 150
2
votes
3
replies
208
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 2 days ago by
Ram
43k • written 2 days ago by
Prawesh
• 0
3
votes
3
replies
217
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 20 hours ago by
ATpoint
82k • written 1 day ago by
Alexandra
• 0
0
votes
3
replies
253
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 2 days ago by
noodle
▴ 580 • written 2 days ago by
doramora
▴ 10
1
vote
3
replies
263
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 11 hours ago by
GenoMax
142k • written 3 days ago by
ohtang7
▴ 40
2
votes
3
replies
276
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
3 days ago by
Azra
▴ 10
0
votes
3
replies
159
views
Merge clusters in Seurat UMAP
seurat
umap
updated 6 hours ago by
Ram
43k • written 9 hours ago by
kilcdincer
▴ 10
1
vote
3
replies
274
views
Using ggplotly in R
ggplot
ggplotly
updated 1 day ago by
jared.andrews07
★ 16k • written 2 days ago by
jen
▴ 10
1
vote
3
replies
182
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 6 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
0
votes
3
replies
190
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 3 days ago by
Ram
43k • written 3 days ago by
yau
• 0
2
votes
3
replies
272
views
Finding variants within a subset of a BAM file
variant
calling
2 days ago by
ramiro.barrantes
• 0
0
votes
3
replies
209
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 2 days ago by
GenoMax
142k • written 3 days ago by
RNAseqer
▴ 270
0
votes
3
replies
199
views
How to access GWAVA software of data
GWAVA
updated 2 days ago by
GenoMax
142k • written 2 days ago by
nonaddldy
▴ 10
0
votes
3
replies
342
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
1
vote
3
replies
182
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 1 day ago by
shpak.max
▴ 50
3
votes
3
replies
264
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 3 days ago by
Ram
43k • written 16 days ago by
Adyasha
• 0
3
votes
2
replies
187
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 3 days ago by
ATpoint
82k • written 3 days ago by
jennyp0706
• 0
0
votes
2
replies
230
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
6 days ago by
jain72744
▴ 10
0
votes
2
replies
270
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 6 days ago by
GenoMax
142k • written 13 days ago by
Ximena
• 0
0
votes
2
replies
228
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 6 days ago by
Ram
43k • written 7 days ago by
sainavyav22
• 0
0
votes
2
replies
293
views
How are score_weights calculated in this code?
single-cell
5 days ago by
carolofharvest
▴ 40
0
votes
2
replies
230
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 8 days ago by
elisheva
▴ 120
0
votes
2
replies
295
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 13 days ago by
yahn
• 0
0
votes
2
replies
229
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
3 days ago by
analyst
▴ 50
0
votes
2
replies
207
views
Output file of samtools flagstat empty
samtools-flagstat
updated 3 days ago by
colindaven
6.4k • written 4 days ago by
ramendra.sarma
• 0
1
vote
2
replies
358
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 3 days ago by
Ram
43k • written 4 days ago by
t.fortunato.asquini
• 0
1
vote
2
replies
177
views
Duplicated sequence samtools
bowtie2
samtools
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Moinuddin
• 0
0
votes
2
replies
423
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
3 days ago by
David Langenberger
11k
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 3 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
3
votes
2
replies
276
views
imputation through beagle
panel
beagle
reference
imputation
2 days ago by
analyst
▴ 50
0
votes
2
replies
175
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
2 days ago by
IdaHao0921
• 0
1
vote
2
replies
262
views
How to interpret infinite odds ratio?
statistics
2 days ago by
Lukas
• 0
189 results • Page
2 of 4
Recent Votes
Comment: switch off warning in blast command line
Forward And Reverse Strand Conventions
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 10
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test
by
Nyksubuz
▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range
by
Nyksubuz
▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem
by
saifulislam99121
• 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite
by
dario.garvan
▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
GenoMax
142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo.
by
Ram
43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
txema.heredia
▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
swbarnes2
14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
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