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832 results • Page
5 of 17
Sort: Votes
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Views
Votes
Replies
2
votes
3
replies
512
views
Website or tool to obtain a list of genes that participate in a specific process?
genomics
updated 1 day ago by
NancyTLi
• 0 • written 3 months ago by
Hamtaro
▴ 50
2
votes
6
replies
462
views
single cell RNA seq integration(Error in UseMethod(generic = "as.sparse", object = x))
scRNA-seq
20 days ago by
kayah
• 0
2
votes
3
replies
330
views
STAR alignment setting for RNA-Seq data from mouse background expressing a human ortholog
alignment
star
ortholog
rna-seq
updated 22 days ago by
swbarnes2
14k • written 22 days ago by
marionette.kent
• 0
2
votes
2
replies
126
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 16 hours ago by
dariober
14k • written 22 hours ago by
Pumla
• 0
2
votes
5
replies
521
views
Weird Fragment Length distribution multiQC
Salmon
RNA-seq
paired-end
MultiQC
updated 17 days ago by
GenoMax
140k • written 28 days ago by
_deb
• 0
2
votes
5
replies
385
views
How to add FORMAT/TAG = "." to all samples in a vcf file via bcftools?
vcf
bcftools
updated 8 days ago by
Pierre Lindenbaum
160k • written 9 days ago by
Марта
• 0
2
votes
2
replies
229
views
singlecell annotation
scRNA-seq
annotation
2 days ago by
kayah
• 0
2
votes
3
replies
377
views
Practical Haplotype Graph
methodID
PHG
updated 28 days ago by
lcj34
▴ 410 • written 4 weeks ago by
yifangt86
▴ 60
2
votes
3
replies
782
views
Inflation in Imputed data
genomic
immunochip
inflation
topmed
updated 20 days ago by
Amy
▴ 20 • written 22 months ago by
desicasares
▴ 40
2
votes
1
reply
196
views
Choosing an FC Threshold
statistics
rna-seq
updated 1 day ago by
Gordon Smyth
★ 6.9k • written 2 days ago by
Netanel
• 0
2
votes
2
replies
221
views
Infering the cell composition from bulk RNA-seq data for mouse
RNA-seq
deconvolution
mouse
6 days ago by
feather-W
• 0
2
votes
3
replies
352
views
HLA genotyping of whole genome sequencing data
HLA
genotyping
WGS
29 days ago by
Biomed-jeh
• 0
2
votes
4
replies
524
views
If the mane transcript isn't available should you use the canonical transcript?
ensembl
mane
gnomad
canonical
21 days ago by
amy__
▴ 160
2
votes
5
replies
455
views
How do I use md5sum to check if my .fastq files from SRA Explorer have been downloaded correctly
scRNA-seq
md5
updated 27 days ago by
ATpoint
81k • written 6 weeks ago by
biotrekker
▴ 100
2
votes
8
replies
1.2k
views
How can I linearize certain residues within an existing protein structure to create a dumbbell-shaped structure?
pymol
python
biopython
structural-bioinformatics
updated 23 days ago by
Wayne
★ 1.9k • written 5 weeks ago by
Aman Vishwakarma
• 0
2
votes
5
replies
608
views
I am trying to generate a bcf file through samtools mpileup but it taking too long, how long does it usually take to generate a bcf file?
alignment
sam
Bam
samtools
Bioinformatics
updated 14 days ago by
jkbonfield
★ 1.2k • written 15 days ago by
K
• 0
2
votes
3
replies
326
views
representing PCs as marginal distribution on x and Y acis
PCAtool
Deseq2
Pcaplot
PCA
updated 12 days ago by
Papyrus
★ 2.9k • written 13 days ago by
Yogesh
• 0
2
votes
8
replies
263
views
Piping samtools to R
R
NGS
bash
samtools
1 day ago by
joe
▴ 470
2
votes
5
replies
393
views
How to root this tree?
Phylogeny
Tree
Root
updated 29 days ago by
Michael
54k • written 29 days ago by
Mirko
• 0
2
votes
2
replies
263
views
compare dimplot(single cell)
DEG
scRNAseq
13 days ago by
kayah
• 0
2
votes
10
replies
560
views
Can't properly use GATK Mutect2 to call somatic variants from my tumor/normal samples pair (BAM to VCF)
vaf
gatk
vcf
genomics
mutect2
updated 15 days ago by
GenoMax
140k • written 16 days ago by
Samuel
▴ 20
2
votes
2
replies
257
views
Annotating indels and SNVs
annotation
indels
SNV
7 days ago by
am29
▴ 30
2
votes
1
reply
301
views
Tool:
TGSFilter, An ultra-fast and efficient tool for long reads filtering and trimming
genome-assembly
filtering
reads
trimming
updated 4 days ago by
Yingzi
• 0 • written 5 days ago by
Huiyang
▴ 180
2
votes
1
reply
219
views
ATAC-seq downstream analysis
ATAC-seq
diffbind
updated 29 days ago by
ATpoint
81k • written 4 weeks ago by
maplewj
▴ 10
2
votes
6
replies
453
views
Need help understanding core SNPs
SNPs
snippy
3 days ago by
ujichu
• 0
2
votes
2
replies
216
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 1 day ago by
Pierre Lindenbaum
160k • written 2 days ago by
fred.s.kremer
▴ 110
2
votes
3
replies
246
views
Read length distribution of whole genome sequnces of human
fastq
read
fastqc
8 days ago by
Yellapu
• 0
2
votes
1
reply
143
views
Computing the neighborhood graph in single cell pipeline
single-cell
knn
updated 17 days ago by
ATpoint
81k • written 17 days ago by
QX
• 0
2
votes
3
replies
240
views
Annotate genes from gtf file to vcf file
gtf
genomics
vcf
7 days ago by
QX
• 0
2
votes
2
replies
214
views
Seeking Help with Cell Ranger Multi Error in fixed-RNA-profiling
chromium
fixed-RNA-profiling
cellranger
updated 7 days ago by
naveau
• 0 • written 14 days ago by
lam
▴ 10
2
votes
7
replies
599
views
Selecting query format for repeated calls to NCBI's API
NCBI
esummary
elink
API
efetch
updated 3 days ago by
GenoMax
140k • written 5 weeks ago by
LauferVA
4.1k
2
votes
5
replies
452
views
Searching for gene in multiple genomes
gene
genome
alignment
sequence
updated 6 days ago by
BioinfGuru
★ 1.6k • written 7 days ago by
Miya
• 0
2
votes
2
replies
229
views
Error from cgat gtf2gtf --method=genes-to-unique-chunks
RNA-Seq
GTF
cgat
27 days ago by
barrypraveen
▴ 130
2
votes
8
replies
441
views
Expert Guidance Required for De Novo Transcriptome Analysis
Transcriptome
De-novo
updated 8 days ago by
GenoMax
140k • written 10 days ago by
ben@f
▴ 10
2
votes
3
replies
313
views
GnomAD
gnomAD
27 days ago by
ananta.kapoor
• 0
2
votes
1
reply
1.1k
views
Using the ranking value to filter
discosnp
RNA-Seq
variant-calling
updated 2 days ago by
Ram
43k • written 6.0 years ago by
vguerracanedo
▴ 10
2
votes
4
replies
258
views
repeatseq compilation issues
NGS
Repeats
repeatseq
repeatexpansion
Genomics
updated 16 days ago by
Michael
54k • written 17 days ago by
adarsh_pp
▴ 40
2
votes
11
replies
804
views
RNA seq aligner?
Alignment
4 days ago by
tesfaye
• 0
2
votes
3
replies
213
views
Reference mouse phased vcf
mm10
vcf
phasing
Beagle
4 days ago by
machoo
• 0
2
votes
3
replies
2.1k
views
Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!!
genome
next-gen
software-error
Assembly
updated 16 hours ago by
Ram
43k • written 4.0 years ago by
memy
▴ 20
2
votes
7
replies
525
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq
contamination
updated 15 days ago by
Chris Dean
▴ 390 • written 16 days ago by
ev97
▴ 20
2
votes
5
replies
426
views
minimap2 gets killed, but it doesn't explain why
bowtie2
updated 27 days ago by
i.sudbery
18k • written 28 days ago by
michael.flower.14
▴ 180
2
votes
1
reply
301
views
GIS overlay for environmental samples from NCBI
NCBI
environmental
SRA
GIS
ArcPro
6 days ago by
joe
▴ 470
2
votes
2
replies
143
views
Interproscan taking so much time
slurm
interproscan
transcriptomics
updated 22 hours ago by
dthorbur
★ 1.7k • written 22 hours ago by
Mohamed Abderrahmane
▴ 10
2
votes
3
replies
354
views
Variant caller for Ion Torrent data
ThermoFisher
NGS
IonTorrent
Genomics
Variant-Calling
updated 19 days ago by
Brian Bushnell
20k • written 21 days ago by
adarsh_pp
▴ 40
2
votes
1
reply
275
views
DESeq and SVA for batch effect
sva
limma
batch-effect
DESeq2
updated 21 days ago by
LChart
3.9k • written 22 days ago by
michelafrancesconi9
▴ 20
2
votes
4
replies
349
views
Subsetting Seurat object based on list of cell barcodes
seurat
updated 10 days ago by
Ming Tommy Tang
★ 3.9k • written 10 days ago by
bgbs
• 0
2
votes
3
replies
242
views
Extracting information from my VCF file
VCF
updated 2 days ago by
bioruffo
▴ 40 • written 2 days ago by
realtreeecat
• 0
2
votes
1
reply
209
views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated 7 days ago by
Ram
43k • written 8 days ago by
Shicheng Guo
★ 9.4k
2
votes
1
reply
2.5k
views
CRAM reference registry and the GRch38 reference genome
BAM
Samtools
GRCh38
CRAM
Variant-Calling
updated 2 days ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
832 results • Page
5 of 17
Recent Votes
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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