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91 results • Page
2 of 2
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Votes
Replies
0
votes
0
replies
117
views
How to implement an IGV to streamlit app?
python
streamlit
igv
3 days ago by
avigail.shnaider
• 0
0
votes
0
replies
128
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
4 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
117
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
4 days ago by
Christopher
• 0
0
votes
0
replies
119
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
4 days ago by
DGTool
• 0
1
vote
3
replies
242
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 39 minutes ago by
bk11
★ 2.4k • written 4 days ago by
Yoosef
▴ 60
0
votes
1
reply
260
views
creating batch colum for batch correction
batch-correction
combat
3 days ago by
Expert
▴ 10
0
votes
1
reply
217
views
Help with DGEList function
DGEList
R
updated 3 days ago by
marco.barr
▴ 100 • written 5 days ago by
Natali
• 0
0
votes
0
replies
155
views
Homer motif analysis
Homer
5 days ago by
daffodil
▴ 10
0
votes
1
reply
204
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Ximena
• 0
0
votes
1
reply
199
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 5 days ago by
Ram
43k • written 5 days ago by
Valentina
• 0
0
votes
6
replies
426
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
Erina
• 0
1
vote
3
replies
284
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
4 days ago by
Lada
▴ 30
1
vote
0
replies
148
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 3 days ago by
zx8754
11k • written 6 days ago by
Emilie
▴ 10
0
votes
0
replies
138
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
6 days ago by
Javier
• 0
0
votes
1
reply
235
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 5 days ago by
Thanujay S
• 0 • written 6 days ago by
yahn
• 0
0
votes
0
replies
130
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
6 days ago by
mikemakaveli1
• 0
2
votes
2
replies
218
views
Raw counts using stringtie
stringtie
RNA-seq
updated 6 days ago by
GenoMax
142k • written 6 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
131
views
Modify plot R mtDNA indel
plot
mtDNA
R
6 days ago by
marco.barr
▴ 100
0
votes
0
replies
321
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
6 days ago by
NorbertK
▴ 10
0
votes
2
replies
251
views
Downloading older version of a tool
Alignment
tools
5 days ago by
Ruqaiya
• 0
0
votes
0
replies
147
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
6 days ago by
rustykb
▴ 20
3
votes
5
replies
288
views
Generating mpileup file using samtools
mpileup
samtools
updated 6 days ago by
Joe
21k • written 6 days ago by
Ruqaiya
• 0
2
votes
3
replies
293
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 6 days ago by
dthorbur
★ 1.9k • written 6 days ago by
Vijith
▴ 30
0
votes
0
replies
148
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
6 days ago by
Jeyong
• 0
0
votes
0
replies
135
views
Empty table plot using plotGseaTable()
FGSEA
5 days ago by
Chris
▴ 280
3
votes
8
replies
520
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
3 days ago by
Qroid
▴ 40
1
vote
3
replies
247
views
Odd alignment question/finding
Alignment
updated 6 days ago by
barslmn
★ 2.1k • written 7 days ago by
poordumbsillyidiot
• 0
0
votes
2
replies
231
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
2 days ago by
Ahiad Chen Zion
• 0
3
votes
3
replies
230
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 days ago by
Adyasha
• 0
1
vote
2
replies
241
views
Downloading full alignments from Pfam
pfam
4 days ago by
bef1
• 0
0
votes
4
replies
380
views
Highest variable features in single cell data
single-cell
2 days ago by
carolofharvest
▴ 40
1
vote
6
replies
358
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 6 days ago by
GenoMax
142k • written 24 days ago by
eebloom
▴ 80
1
vote
0
replies
170
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
4 hours ago by
eebloom
▴ 80
0
votes
2
replies
248
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
1 day ago by
sainavyav22
• 0
0
votes
0
replies
179
views
CellPhoneDB results
cellphonedb
cpdb
cell_surface_proteins
updated 2 days ago by
GenoMax
142k • written 10 weeks ago by
piotto
▴ 20
1
vote
3
replies
388
views
cellranger error message
multiplexing
cellranger
updated 1 hour ago by
Max
• 0 • written 12 weeks ago by
Alivia
▴ 10
0
votes
1
reply
547
views
HOMER on AWS
HOMER
updated 6 days ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 6 days ago by
e.r.zakiev
▴ 210 • written 3.8 years ago by
n.anuragsharma
▴ 40
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 6 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 3 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 5 days ago by
Ruqaiya
• 0 • written 10.2 years ago by
Yuelin
▴ 20
91 results • Page
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Recent Votes
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
cellranger error message
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Network plot from expression data in R using igraph
Comment: RNA seq analysis
RNA seq analysis
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3.6k
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tim.booth
▴ 50
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Comment: Different output for read length
by
Pierre Lindenbaum
161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
bk11
★ 2.4k
Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length
by
marco.barr
▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
Comment: Different output for read length
by
marco.barr
▴ 100
I just published my link on paste, why can't I see my public paste on the site?
Comment: cellranger error message
by
Max
• 0
I'm having a similar issue. The sample_id matches the filename prefix before _S1_L001, but I get the error: Log message: Requested sample(s…
Comment: Different output for read length
by
marco.barr
▴ 100
Thanks so much GenoMax, I'm sharing the link as you told me
Comment: Different output for read length
by
GenoMax
142k
Post the data at pastebin.com and add a link here or you could a GitHub gist. You were suspended by biostars SPAM bot since you pasted link…
Comment: Different output for read length
by
GenoMax
142k
Post the data at pastebin.com and add the link here. You were suspended by biostars SPAM bot since you pasted these links in quick successi…
Comment: RNA seq analysis
by
s.ghazala
• 0
Could you clarify on what exactly you are referring to with "SRA data table". If you are retrieving fastq files (raw data), then you could …
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 100
Thanks, Chris. I really appreciate your help. This has clarified a lot for me!
Answer: Snakemake fails to find conda in PBS
by
tim.booth
▴ 50
Snakemake does not have support for micromamba. There is an open issue: https://github.com/snakemake/snakemake/issues/2322
Comment: absolute path for symbolic links in Snakefile
by
tim.booth
▴ 50
Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
Answer: Different output for read length
by
Pierre Lindenbaum
161k
I supect your reads are hard clipped. Show us the first lines of samtools view /home/sorted.bam | cut -f 2,6,10 | head -n 20
Comment: Presence of unknown sites in ANNOVAR output file
by
sainavyav22
• 0
Here you go. 1.perl convert2annovar.pl -format vcf4old 1008_Tumor.vcf > 1008Tumor_variant.avinput 2.perl annotate_variation.pl 100…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Jeremy Leipzig
22k
Those are samples. If a sample has a 0/1 or a 1/1 genotype for that variant, they have the variant. Your question is ambiguous because you…
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