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834 results • Page
4 of 17
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Votes
Replies
0
votes
12
replies
774
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
3 days ago by
biwdpang
• 0
0
votes
0
replies
148
views
Cromwell slurm singularity call caching
cromwell
singularity
wdl
5 days ago by
asmariyaz23
▴ 10
0
votes
1
reply
203
views
Getting error in alignment using STAR
STAR
Error
updated 5 days ago by
Michael
54k • written 5 days ago by
pavithra.bioinformatics
• 0
0
votes
1
reply
1.8k
views
Speed up PHASE software for haplotype inference
multithreading
unix
haplotype
updated 5 days ago by
WANG
• 0 • written 8.2 years ago by
kshitijtayal
▴ 40
2
votes
1
reply
301
views
GIS overlay for environmental samples from NCBI
NCBI
environmental
SRA
GIS
ArcPro
6 days ago by
joe
▴ 470
0
votes
1
reply
226
views
PCA script correction
correction
script
PCA
updated 6 days ago by
BioinfGuru
★ 1.6k • written 6 days ago by
prity6459
• 0
3
votes
5
replies
381
views
Losing my mind with a VCF problem
vcf
bcftools
updated 6 days ago by
Michael
54k • written 6 days ago by
a.beggs
▴ 30
1
vote
13
replies
965
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 3 days ago by
lcj34
▴ 410 • written 9 days ago by
b.contreras.moreira
▴ 70
0
votes
2
replies
290
views
PopGenome lost individual information
PopGenome
2 days ago by
Yixuan
• 0
5
votes
15
replies
4.7k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq
IGV
mapping
updated 6 days ago by
vague-barracuda-4686
• 0 • written 4.7 years ago by
Apprentice
▴ 160
2
votes
6
replies
452
views
Need help understanding core SNPs
SNPs
snippy
3 days ago by
ujichu
• 0
1
vote
1
reply
196
views
genome.fa to indix files to use it in rna-seq analysis
RNA-seq
hisat2
index
updated 6 days ago by
GenoMax
140k • written 6 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
163
views
Tutorial:
Parsing HMMER output
HMMER
updated 6 days ago by
GenoMax
140k • written 6 days ago by
I0110
▴ 130
2
votes
5
replies
451
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
0
votes
0
replies
178
views
Only positive enrichment score in GSEA
enrichmentanalysis
clusterprofiler
gsea
bioconductor
rnaseq
6 days ago by
enee
▴ 10
0
votes
9
replies
458
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 15 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
0
votes
0
replies
164
views
working with shapeit.
shapeit
6 days ago by
sanchit000singhdr098
• 0
0
votes
0
replies
155
views
Motif Scanning: HOMER vs MEME, settings?
homer
fimo
6 days ago by
mb
• 0
0
votes
0
replies
165
views
How to identify the phylogenetic node age of RNAs?
phylogeny
genome
evolution
RNA-seq
6 days ago by
Apex92
▴ 280
0
votes
9
replies
452
views
Intersect genomic locations with genes
fanc
Chromatin
conformation
Hic
hic
updated 6 days ago by
zx8754
11k • written 6 days ago by
naveedhasan2000
• 0
0
votes
3
replies
298
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv
compressing
varscan
bcftools
6 days ago by
kabir.deb
▴ 80
0
votes
0
replies
178
views
Questions on demultiplexing using Qiime2
demultiplexing
barcode
6 days ago by
Minh
• 0
1
vote
3
replies
2.4k
views
How to remove variants with 3+ alleles present Plink1.9
HaplotypeCaller
GATK
Plink1.9
vcftools
updated 6 days ago by
Jingjingzhang
• 0 • written 2.1 years ago by
ramshahaya
▴ 10
0
votes
3
replies
387
views
RNAseq
R
RNA-seq
Linux
6 days ago by
mrymrahimi70
• 0
0
votes
4
replies
496
views
calculating mean fragment length from CollectInsertSizeMetrics(Picard) output
count2fpkm
updated 7 days ago by
ATpoint
81k • written 10 days ago by
Niharika
• 0
2
votes
2
replies
257
views
Annotating indels and SNVs
annotation
indels
SNV
7 days ago by
am29
▴ 30
0
votes
4
replies
333
views
HISAT2 installation issue
HISAT2
updated 7 days ago by
GenoMax
140k • written 7 days ago by
eleven11
• 0
0
votes
8
replies
510
views
Fine-tuning NCBI taxid / taxidlist
BLAST
taxonomy
7 days ago by
theclubstyle
▴ 40
0
votes
0
replies
183
views
Problem encountered during Pearson Correlation Analysis between two immune cell subtypes
scRNA-seq
biostatistics
6 days ago by
applepie
• 0
1
vote
5
replies
443
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications
dorado
basecalling
nanopore
methylation
updated 6 days ago by
LauferVA
4.1k • written 7 days ago by
njornet
▴ 10
0
votes
6
replies
407
views
Download Panther entry list
PANTHER
7 days ago by
Nicolas
• 0
0
votes
0
replies
177
views
Troubleshooting SCTransform Error in Seurat: "Can't use NA as row index in a tibble for assignment"
SCTransform
updated 7 days ago by
Ram
43k • written 7 days ago by
Anisha
• 0
0
votes
0
replies
171
views
scRNA Cell Clustering Defined by Normalized Counts
Normalization
scRNA
Seurat
7 days ago by
sakura
• 0
0
votes
0
replies
173
views
Example - Meta Analysis TCGA and DepMap
Meta-Analysis
TCGA
DepMap
updated 7 days ago by
Ram
43k • written 7 days ago by
joseph.landry
▴ 50
0
votes
4
replies
356
views
bcftools select sites with multiple combinations of FILTER column
bcftools
6 days ago by
User000
▴ 690
0
votes
1
reply
198
views
Extract Umi sequence to readname
Sequence
FgBio
UMI
updated 7 days ago by
GenoMax
140k • written 7 days ago by
Smilesky
• 0
1
vote
3
replies
325
views
Combining and Forward and Reverse Reads
genome
alignment
concatenation
sequencing
4 days ago by
SineWave
• 0
0
votes
1
reply
392
views
Genbank Bacteriophage Genome Submission - Internal stop codons in CDS sequences
CDS
Genome
NCBI
Genbank
updated 7 days ago by
Ram
43k • written 7 weeks ago by
Sowmya Pulapet
▴ 70
0
votes
0
replies
141
views
Blog:
WGBS vs RRBS
RRBS
DNA-methylation
WGBS
updated 7 days ago by
Ram
43k • written 7 days ago by
Novogene
▴ 410
1
vote
6
replies
461
views
Quest about the input data for PCA analysis
PCA
5 days ago by
tujuchuanli
▴ 100
1
vote
2
replies
258
views
How to visualize scRNA-seq normalized data
Seurat
10x
scRNA-Seq
Single-cell
normalization
7 days ago by
SlowSD
• 0
2
votes
1
reply
208
views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated 7 days ago by
Ram
43k • written 7 days ago by
Shicheng Guo
★ 9.4k
15
votes
6
replies
599
views
Need consultation about my rna-seq workflow
RNA-seq
Gene-expression
updated 7 days ago by
Ram
43k • written 9 days ago by
markusz
▴ 10
6
votes
7
replies
623
views
cutadapt not trimming all adapters in PE Illumina sequencing
NGS
Illumina
cutadapt
6 days ago by
joe
▴ 470
0
votes
1
reply
211
views
Using multiple reference genomes for alignment in dorado?
dorado
basecall
ONT
alignment
updated 8 days ago by
GenoMax
140k • written 8 days ago by
gideonav
• 0
0
votes
1
reply
264
views
Automatic protein symmetry classification from PDB coordinates
pdb
symmetry
protein
updated 8 days ago by
Mensur Dlakic
★ 26k • written 9 days ago by
Kartik
• 0
1
vote
7
replies
391
views
'Invalid parameter' error to generate a count matrix using featurecounts
RNA-seq
featurecounts
updated 8 days ago by
GenoMax
140k • written 8 days ago by
Shay
• 0
0
votes
1
reply
289
views
Find out shared differentially expressed genes between two cell lines due to knockdown treatment
expression
RNA
differential
gene
seq
updated 8 days ago by
swbarnes2
14k • written 9 days ago by
Xinqi
• 0
8
votes
16
replies
5.2k
views
9 follow
visualize CNV data based on WGS
CNV
updated 8 days ago by
clealk
▴ 50 • written 6.2 years ago by
Bogdan
★ 1.4k
1
vote
1
reply
175
views
Seeking for edgeR TMM Normalization calcul example
tmm
edgeR
deseq2
updated 8 days ago by
jared.andrews07
★ 16k • written 8 days ago by
Picasa
▴ 640
834 results • Page
4 of 17
Recent Votes
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!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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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…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
Some things never change ... the most common mistake is still the one on top there
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