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121,965 results • Page
208 of 2440
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1
vote
2
replies
1.3k
views
convert bed12 to sorted gtf
bed12
gtf
gff
awk
updated 2.0 years ago by
alejandrogzi
▴ 150 • written 3.2 years ago by
maria
• 0
0
votes
0
replies
791
views
News:
NCBI ClinVar XML update to accommodate somatic variants
SNP
XML
ClinVar
NCBI
21 months ago by
PeterC_NCBI
▴ 520
38
votes
25
replies
12k
views
13 follow
FASTA file of fixed length
sequence
fasta
updated 2.1 years ago by
Ram
45k • written 9.5 years ago by
waqasnayab
▴ 250
0
votes
1
reply
762
views
How many FASTQ files does one SRA Run correspond to?
fastq
sra
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
hamarillo
▴ 80
0
votes
4
replies
2.1k
views
Running Enrichr in python using a background gene list
gp.enrichr
python
Enrichr
2.1 years ago by
Jen
▴ 100
0
votes
3
replies
2.2k
views
Pearson correlation with different row numbers across two datasets?
pearson-correlation
updated 15 months ago by
Ram
45k • written 2.1 years ago by
Faith
▴ 50
2
votes
11
replies
2.5k
views
Extracting regions around sites in VCF file and writing them as fasta sequences/files
VCF
fasta
updated 2.1 years ago by
GenoMax
154k • written 2.1 years ago by
Aiswarya
▴ 20
4
votes
3
replies
1.2k
views
blastn Command Not Found
abricate
linux
blastn
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
2Black_Cats
• 0
3
votes
7
replies
2.7k
views
Nextflow - How to pass the yml format input file from an argument to channel as a list
python
groovy
yaml
nextflow
2.1 years ago by
kani
▴ 10
0
votes
1
reply
849
views
How to generate a consensus sequence from BAM file with bcftools?
bam
bcftools
consensus
updated 2.1 years ago by
GenoMax
154k • written 2.1 years ago by
marongiu.luigi
▴ 760
6
votes
3
replies
954
views
how to remove description from header?
fasta
2.1 years ago by
Sapphire
▴ 10
4
votes
5
replies
3.7k
views
Selecting MOUSE gene set libraries in Enrichr
Enrichr
updated 2.1 years ago by
fracarb8
★ 1.7k • written 2.1 years ago by
Jen
▴ 100
0
votes
0
replies
446
views
OBITools - Problem with obiclean
python
OBITools
metabarcoding
obiclean
2.1 years ago by
Elise
• 0
0
votes
1
reply
1.3k
views
Job:
Looking for Part Time Work as a Compuational Chemist / Bioinformatician / LINUX Admin in the Scientific Community
Python
gatk
gromacs
cp2k
SLURM
updated 2.1 years ago by
colindaven
8.0k • written 2.1 years ago by
sebmuraru
• 0
3
votes
1
reply
944
views
Can I annotate a 32GB vcf file containing 300 samples at once using ANNOVAR?
ANNOVAR
written 2.1 years ago by
christinacanavati2014
• 0
2
votes
2
replies
1.1k
views
functional and genome annotation analysis
deletion
genome-annotation
updated 2.1 years ago by
luffy
▴ 130 • written 2.1 years ago by
bestone
▴ 30
1
vote
2
replies
4.4k
views
bcftools merge is resulting in a lot of missing data, how do I fix this?
vcf
bcf
updated 2.1 years ago by
r.shamsi
• 0 • written 4.5 years ago by
devenvyas
▴ 770
0
votes
0
replies
515
views
News:
Workshop on Virtual Screening on Drug Discovery from scratch (15-16 September, 2023 : 07.00 - 09.00 PM IST)
workshop
virtual-screening
updated 24 months ago by
Ram
45k • written 2.1 years ago by
sriv.reetesh
• 0
0
votes
1
reply
1.1k
views
Tutorial:
TAPIS installation and usage
APA
Iso-seq
splicing
TAPIS
analysis
alternative
updated 2.1 years ago by
ATpoint
89k • written 2.1 years ago by
JC
▴ 30
0
votes
0
replies
580
views
News:
RNAseq data analysis with R/Bioconductor
R
RNA-seq
Bioconductor
updated 24 months ago by
Ram
45k • written 2.1 years ago by
Physalia-courses
★ 2.6k
2
votes
3
replies
1.2k
views
How best can I find transposons in my genome?
transposons
updated 2.1 years ago by
Philipp Bayer
8.9k • written 2.1 years ago by
eennadi
▴ 40
0
votes
1
reply
678
views
Is it okay to normalize data once more?
scRNA
normalization
updated 2.1 years ago by
biofalconch
★ 1.3k • written 2.1 years ago by
le93jk
• 0
1
vote
2
replies
1.6k
views
bcftools view -r issue
bcftools
updated 2.1 years ago by
John Marshall
3.1k • written 2.1 years ago by
ayh
• 0
3
votes
3
replies
1.6k
views
Why is my genome assembly not aligning well?
alignment
2.1 years ago by
eennadi
▴ 40
0
votes
0
replies
553
views
Long-reads assembly using Miniasm in NanoGalaxy
assembly
Galaxy
metabarcoding
Nanopore
2.1 years ago by
Cedrick
• 0
0
votes
0
replies
494
views
Ballgown Error
R
Ballgown
Rstudio
updated 2.1 years ago by
zx8754
12k • written 2.1 years ago by
SHXVRR
▴ 20
0
votes
0
replies
520
views
Install packages in old version Julia
package
Julia
2.1 years ago by
sooni
▴ 20
0
votes
2
replies
1.6k
views
How to run TRUST4 for BCR/TCR detection using 10X data?
immunology
trust4
illumina
10x
2.1 years ago by
O.rka
▴ 750
8
votes
5
replies
1.6k
views
Alphafold Cat
Joke
updated 2.0 years ago by
fishgolden
▴ 520 • written 2.1 years ago by
BioGrad321
• 0
3
votes
1
reply
1.0k
views
Overlapping cluster/annotation
Single-Cell
updated 2.1 years ago by
LChart
5.1k • written 2.1 years ago by
synat.keam
▴ 120
0
votes
1
reply
992
views
Drawing label around clusters
cells
Single
updated 2.1 years ago by
Mensur Dlakic
★ 30k • written 2.1 years ago by
synat.keam
▴ 120
0
votes
2
replies
1.2k
views
Explanation needed for POD5 files- channel ID's, PromethION run
promethion
dorado
duplex
ont
pod5
updated 2.1 years ago by
GenoMax
154k • written 2.1 years ago by
carla.finn
• 0
5
votes
5
replies
3.5k
views
How to distinguish between normal and malignant epithelial cells based on CNV?
scRNA-seq
r
CNV
infercnv
CNA
updated 2.1 years ago by
LChart
5.1k • written 2.1 years ago by
fifty_fifty
▴ 90
0
votes
2
replies
1.1k
views
Segmentation fault error in CONTROL-FREEC
copy-number-variants
FREEC
2.1 years ago by
DdogBoss
▴ 20
1
vote
4
replies
1.1k
views
htseq-count reports count values for deleted genes
rna-seq
htseq
2.1 years ago by
kmyers2
▴ 90
3
votes
6
replies
1.8k
views
summarize consecutive columns over a data frame
tidyverse
r
offtopic
updated 2.0 years ago by
Ram
45k • written 2.1 years ago by
Assa Yeroslaviz
★ 1.9k
0
votes
3
replies
1.1k
views
Extracting/assembling organellar reads from RNAseq data
transcriptome
star
alignment
mapping
updated 2.0 years ago by
LChart
5.1k • written 2.1 years ago by
Miles
• 0
0
votes
0
replies
550
views
Help with Mofa2
multiome
mofa2
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
Chris
▴ 360
1
vote
2
replies
1.1k
views
Problem with Mageck paired analysis
Mageck
updated 2.1 years ago by
Meisam
▴ 250 • written 2.1 years ago by
toma.85
• 0
1
vote
3
replies
1.1k
views
Question regarding MACS2 approach of peak calling
MACS2
sequencing-depth
chipseq
updated 2.0 years ago by
ATpoint
89k • written 2.1 years ago by
rkc5
• 0
0
votes
1
reply
999
views
Choosing background for ORA using scrnaseq
scRNA-seq
RNA-seq
ORA
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
rohitsatyam102
▴ 940
3
votes
2
replies
1.5k
views
Best pipeline / resources / tools for whole genome assembly in a haploid organism
haploid
sequencing
genomics
nanopore
wgs
updated 2.1 years ago by
Dave Carlson
★ 2.2k • written 2.1 years ago by
Mark
▴ 60
2
votes
3
replies
1.8k
views
10X scRNA-seq v2 odd fastq format
10x
scRNA-Seq
updated 2.1 years ago by
Ming Tommy Tang
★ 4.7k • written 2.1 years ago by
Dave Carlson
★ 2.2k
10
votes
8
replies
16k
views
8 follow
How to install gdc-client in Ubnutu
ubuntu
gdc-client
updated 2.1 years ago by
Ram
45k • written 9.1 years ago by
pxf109
▴ 20
0
votes
3
replies
1.8k
views
Michigan Imputation Server low reference overlap
imputation
michigan
updated 2.1 years ago by
bk11
★ 3.1k • written 2.1 years ago by
graeme.thorn
▴ 110
0
votes
0
replies
442
views
Association between genetic mutation and other variables
biomarkers
genetics
updated 2.1 years ago by
Ram
45k • written 2.1 years ago by
InterestedInData
• 0
0
votes
0
replies
954
views
Running Funannotate on Fungal Genome
funannotate
assembly
genomeassembly
denovo
annotation
2.1 years ago by
SomeOne
▴ 240
0
votes
1
reply
1.4k
views
Convert from SDF to FASTA
SDF
molecule
fasta
ML
small
updated 2.1 years ago by
Philipp Bayer
8.9k • written 2.1 years ago by
tpritsky
• 0
1
vote
3
replies
1.6k
views
Ann.vcf format
VCF
VEP
SnpEff
Annotation
2.1 years ago by
JAZMIN CELESTE
• 0
0
votes
0
replies
494
views
[Protein-Protein Interaction Network][STRING DB]
proteome
PPI
bacteria
Network
2.1 years ago by
amresharma1
• 0
121,965 results • Page
208 of 2440
Recent Votes
alternate allele frequency and minor allele frequency
Calculating minor allele frequency for GnomAD VCF file
Hiring FT Remote Nextflow engineer to build ML workflows for cancer genomics
Answer: Gene expression equivalent of polygenic risk score ?
A: TRF output to .gff file
A: GATK ASEReadCounter: Downstream analysis for identifying allele specific express
Comment: Differences between published differential gene expression results and own analy
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Popular Question
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marongiu.luigi
▴ 760
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a615ebfb
▴ 60
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★ 2.1k
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Recent Replies
Comment: How to create a consensus of a contig with samtools or bbmap?
by
lieven.sterck
16k
You assembled a genome using samtools ???? that sounds very weird, if not impossible ... The header (SQ lines) is missing from your file b…
Answer: gnomad par region variants
by
benformatics
4.2k
The XX and XY counts are present on any given variants page.
Comment: Help with Ideathon
by
Mensur Dlakic
★ 30k
I don't see a single question here. Saying `I need your expert help in figuring out how I can make this analysis useful!` is too open-ended…
Comment: Differences between published differential gene expression results and own analy
by
ATpoint
89k
Please link the paper, lets see their methods. With human data it can well be that they included something like surrogate variables to damp…
Comment: Differences between published differential gene expression results and own analy
by
dsull
★ 7.7k
There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
Comment: tximport error (medianLengthOverIsoform)
by
rfran010
★ 1.6k
Is it the version number in your data? e.g. ENST00000415118.1 vs ENST00000415118 could be causing the mismatch?
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
• 0
So is there any correct way for normalisation? I know limma recommends CPM via limma-voom and DESeq2 just takes in raw counts and does thei…
Comment: Gene expression equivalent of polygenic risk score ?
by
Picasa
▴ 690
Thanks a lot for your answer. I will check the paper.
Comment: Differences between published differential gene expression results and own analy
by
dsull
★ 7.7k
If those logFCs are different, then that's a normalization issue. The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
• 0
Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
• 0
Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
Comment: Errors with RSEM/bowtie2
by
Olivia
• 0
I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
Answer: Gene expression equivalent of polygenic risk score ?
by
GouthamAtla
12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
Comment: ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues usin
by
Ben
• 0
write.table(df1, "df1.txt", sep = "\t", row.names = T, col.names = T, quote = FALSE)
Comment: Errors with RSEM/bowtie2
by
GenoMax
154k
That is good confirmation. Bacl to the error message. > I don't know how to fix this, given that I already did the trimming steps. DId yo…
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