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187 results • Page
2 of 4
Sort: replies
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Views
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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
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
2
votes
4
replies
256
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 1 day ago by
yura.grabovska
▴ 90 • written 1 day ago by
ev97
▴ 20
0
votes
4
replies
257
views
Galaxy StringTie error
stringtie
galaxy
3 days ago by
trkfs
• 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
3
votes
4
replies
248
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
genome
updated 19 hours ago by
Ram
43k • written 1 day ago by
Ali
• 0
2
votes
4
replies
218
views
Help with IGV abbreviation
igv
updated 2 days ago by
Ram
43k • written 3 days ago by
GeneC
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 2 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
1
vote
4
replies
341
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
2
votes
4
replies
292
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
2 days ago by
Esraa
• 0
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
278
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
1 day ago by
Arton
▴ 10
3
votes
3
replies
222
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 1 day ago by
ATpoint
82k • written 2 days ago by
Alexandra
• 0
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
0
votes
3
replies
255
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 2 days ago by
noodle
▴ 580 • written 2 days ago by
doramora
▴ 10
3
votes
3
replies
166
views
getting exon coordinates
genomics
updated 19 hours ago by
Ram
43k • written 20 hours ago by
Xbox_27
• 0
2
votes
3
replies
277
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
4 days ago by
Azra
▴ 10
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
1
vote
3
replies
266
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 16 hours ago by
GenoMax
142k • written 3 days ago by
ohtang7
▴ 40
1
vote
3
replies
189
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
0
votes
3
replies
161
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
1 day ago by
Esraa
• 0
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
342
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
3
votes
3
replies
266
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 3 days ago by
Ram
43k • written 17 days ago by
Adyasha
• 0
0
votes
3
replies
200
views
How to access GWAVA software of data
GWAVA
updated 2 days ago by
GenoMax
142k • written 3 days ago by
nonaddldy
▴ 10
3
votes
3
replies
280
views
what is another word for a BLAST "hit"?
blast
alignment
6 days ago by
dec986
▴ 380
0
votes
3
replies
193
views
Sam file Header problem
Sam
Header
problem
file
updated 3 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
saifulislam99121
• 0
2
votes
3
replies
198
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 11 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
0
votes
3
replies
210
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 2 days ago by
GenoMax
142k • written 3 days ago by
RNAseqer
▴ 270
1
vote
3
replies
432
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
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
1
vote
3
replies
793
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 15 hours ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
3
votes
3
replies
358
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 3 days ago by
Mathew
▴ 140 • written 6 days ago by
Christopher
• 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
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
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
3
votes
2
replies
189
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 4 days ago by
ATpoint
82k • written 4 days ago by
jennyp0706
• 0
0
votes
2
replies
424
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
0
votes
2
replies
220
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
1 day ago by
Chen
• 0
0
votes
2
replies
293
views
How are score_weights calculated in this code?
single-cell
6 days ago by
carolofharvest
▴ 40
1
vote
2
replies
178
views
Duplicated sequence samtools
bowtie2
samtools
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Moinuddin
• 0
1
vote
2
replies
222
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
18 hours ago by
bioinfo
▴ 150
0
votes
2
replies
209
views
Output file of samtools flagstat empty
samtools-flagstat
updated 4 days ago by
colindaven
6.4k • written 4 days ago by
ramendra.sarma
• 0
2
votes
2
replies
180
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 19 hours ago by
Ram
43k • written 1 day ago by
jsmith120f
• 0
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
2
votes
2
replies
193
views
genome finishing
finishing
genome
updated 1 day ago by
nd48
▴ 20 • written 1 day ago by
trezini
• 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
186
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
2 days ago by
melissa.joubert
• 0
2
votes
2
replies
171
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 14 hours ago by
Ram
43k • written 16 hours ago by
txema.heredia
▴ 130
3
votes
2
replies
278
views
imputation through beagle
panel
beagle
reference
imputation
3 days ago by
analyst
▴ 50
187 results • Page
2 of 4
Recent Votes
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
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Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input?
by
Pierre Lindenbaum
161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem
by
Pierre Lindenbaum
161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
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by
DGTool
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I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
b.contreras.moreira
▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input?
by
LucisTheFather
• 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
thank you
Comment: How to extract cells of different species after mapping with combined genome?
by
Tony
• 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 20
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
▴ 20
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
▴ 20
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?
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