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482 results • Page
3 of 10
Sort: Votes
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Views
Votes
Replies
1
vote
0
replies
172
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
8 days ago by
rohitsatyam102
▴ 850
1
vote
4
replies
391
views
Molecular docking with Autodock
Docking
proteomics
updated 28 days ago by
Ram
43k • written 3 months ago by
shwetamgr1
▴ 10
1
vote
1
reply
475
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
14 days ago by
renan.igor
• 0
1
vote
2
replies
336
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 18 days ago by
Istvan Albert
100k • written 19 days ago by
Jiang
• 0
1
vote
3
replies
299
views
True variants selection
vcf
bcftools
updated 21 days ago by
dthorbur
★ 1.9k • written 22 days ago by
maevalefeuvre
• 0
1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva
microarrays
batch-effect
updated 16 days ago by
Ram
43k • written 6.8 years ago by
ATCG
▴ 380
1
vote
1
reply
601
views
accessing the global gut microbial gene catalogue (MEDUSA)
medusa
gene-catalogue
gut-microbiome
updated 22 days ago by
Ram
43k • written 3.3 years ago by
ramin.k2013
• 0
1
vote
4
replies
1.4k
views
Splitting long reads into shorter chunks
long-read
updated 28 days ago by
Ram
43k • written 5.8 years ago by
pennakiza
▴ 60
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 16 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
1
vote
2
replies
220
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 3 days ago by
Ram
43k • written 3 days ago by
Ravita
• 0
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 16 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
1
vote
1
reply
203
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
18 days ago by
CTLong
▴ 110
1
vote
2
replies
215
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
25 days ago by
phhelou5
• 0
1
vote
3
replies
254
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
10 days ago by
WouterDeCoster
47k
1
vote
2
replies
938
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 28 days ago by
Ram
43k • written 24 months ago by
ved_vyas
▴ 20
1
vote
3
replies
378
views
PCA plot
DESeq2
PCAplot
updated 5 days ago by
LauferVA
4.2k • written 8 days ago by
Aaliya
▴ 10
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 1 day ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
1
vote
3
replies
211
views
Odd alignment question/finding
Alignment
updated 13 hours ago by
barslmn
★ 2.1k • written 1 day ago by
poordumbsillyidiot
• 0
1
vote
0
replies
372
views
Differential expression analysis on multiple integrated datasets
microarray
Z-score
limma
differential-gene-expression
meta-analysis
updated 24 days ago by
Ram
43k • written 2.4 years ago by
michael.s
▴ 10
1
vote
2
replies
277
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
2 days ago by
Nafi
• 0
1
vote
3
replies
383
views
Ensembl gene id conversion
biomart
ensembl
updated 17 days ago by
ATpoint
82k • written 19 days ago by
naveedhasan2000
• 0
1
vote
3
replies
265
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 3 days ago by
GenoMax
142k • written 3 days ago by
jeffrey.maurer.informatics
• 0
1
vote
0
replies
165
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
22 days ago by
eebloom
▴ 80
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 18 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
1
vote
0
replies
678
views
Conditions for valid batch effect correction
r
batch-effect
updated 16 days ago by
Ram
43k • written 5.2 years ago by
Sebastian Hesse
▴ 340
1
vote
1
reply
243
views
Retrieve a % coverage for each transcript
RNA-seq
updated 16 days ago by
Ram
43k • written 16 days ago by
jammydodger123456
▴ 40
1
vote
1
reply
841
views
Question for 3 prime bias in rna short read and long read (illumina, ont, pacbio)
rna-seq
short-read
long-read
updated 28 days ago by
Ram
43k • written 11 months ago by
shinyjj
▴ 50
1
vote
2
replies
255
views
permutation test in edgeR
rna-seq
edgeR
updated 11 days ago by
Gordon Smyth
★ 7.1k • written 25 days ago by
Netanel
• 0
1
vote
2
replies
302
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 16 days ago by
Ram
43k • written 16 days ago by
aniigodwinn
• 0
0
votes
2
replies
281
views
Regions not clear in VCF
whole-exome
variant-calling
updated 25 days ago by
Ram
43k • written 26 days ago by
priya.bmg
▴ 60
0
votes
0
replies
193
views
KaryoPlot: Gene coverage over centromeric regions
Gene
coverage
Centromere
Bedtools
21 days ago by
Mary
• 0
0
votes
5
replies
360
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
9 days ago by
njornet
▴ 20
0
votes
0
replies
115
views
Extracting tcga images for cnn in r
rstudio
python
tcga-lihc
svs
29 days ago by
jain72744
▴ 10
0
votes
0
replies
199
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
15 days ago by
synat.keam
▴ 100
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 23 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
5
replies
2.1k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
batch-effect
normalization
updated 17 days ago by
Ram
43k • written 21 months ago by
mmitra
▴ 60
0
votes
0
replies
110
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
3 days ago by
Adyasha
• 0
0
votes
1
reply
180
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 10 days ago by
bk11
★ 2.4k • written 10 days ago by
alphaflylizard
• 0
0
votes
2
replies
98
views
Raw counts using stringtie
stringtie
RNA-seq
updated 6 hours ago by
GenoMax
142k • written 8 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
200
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
14 days ago by
Nitin
• 0
0
votes
0
replies
226
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 15 days ago by
Ram
43k • written 15 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
263
views
Annovar using R package
Annovar
gnomAD
R
8 days ago by
DKA
▴ 40
0
votes
1
reply
136
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 2 days ago by
Ram
43k • written 2 days ago by
ernestine.kubi
• 0
0
votes
0
replies
129
views
DESeq2 LRT divergent DEGs ?
interaction
LRT
deseq2
24 days ago by
klervi-lugue
• 0
0
votes
3
replies
279
views
rRNA depletion of RIP-seq samples
rRNA
RIP-seq
updated 24 days ago by
noodle
▴ 580 • written 24 days ago by
CrisRisu
• 0
0
votes
0
replies
177
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
8 days ago by
simplitia
▴ 130
0
votes
0
replies
598
views
Avoid genome circularization with Canu assembler
circularization
ONT
Canu
repetitive-regions
assembler
updated 28 days ago by
Ram
43k • written 2.9 years ago by
Maria
• 0
0
votes
1
reply
194
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA
substitution
VCFstats
Evolution
VCF
updated 23 days ago by
Pierre Lindenbaum
161k • written 23 days ago by
Saran
▴ 50
0
votes
2
replies
332
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
20 days ago by
O.rka
▴ 710
0
votes
1
reply
224
views
Best way to add alter fastq file by adding short repeats
fastq
updated 28 days ago by
GenoMax
142k • written 28 days ago by
pairedttest
▴ 10
482 results • Page
3 of 10
Recent Votes
Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
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Answer: visualize GSEA
by
bk11
★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
swbarnes2
14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
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Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme
by
e.r.zakiev
▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ
by
GenoMax
142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
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