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327 results • Page
3 of 7
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
189
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
12 days ago by
juliviglino
• 0
0
votes
1
reply
215
views
Esearch, Epost, and Efetch for Large Datasets in Biopython
eutils
biopython
entrez
updated 12 days ago by
Ram
40k • written 13 days ago by
Salem
• 0
3
votes
10
replies
551
views
STAR index not working
STAR
RNA-Seq
12 days ago by
camillab.
▴ 140
2
votes
3
replies
299
views
Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication
apoptosis
updated 13 days ago by
Ram
40k • written 13 days ago by
txema.heredia
▴ 80
0
votes
1
reply
178
views
Prank checkpoint and restore?
prank
alignment
updated 13 days ago by
Ram
40k • written 13 days ago by
Pit
• 0
0
votes
13
replies
611
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
10 days ago by
Y
• 0
1
vote
3
replies
259
views
Sub-sampleing bam files based on sequencing_summary.txt (guppy output)
samtools
guppy
updated 13 days ago by
GenoMax
135k • written 13 days ago by
anika.john
• 0
0
votes
0
replies
124
views
Any way to predict hormone biosynthesis pathways in understudied organisms?
genomics
orthologs
biosynthesis-pathway
updated 13 days ago by
Ram
40k • written 13 days ago by
Mark
• 0
2
votes
4
replies
339
views
Refseq annotation | Populus trichocarpa
R
RNA-seq
plants
Refseq
updated 13 days ago by
Ram
40k • written 13 days ago by
P
• 0
1
vote
1
reply
211
views
Read Counts from BAM file
bam
samtools
qualimap
readcount
updated 13 days ago by
ATpoint
77k • written 13 days ago by
Smriti
▴ 10
0
votes
2
replies
247
views
Is it okay to just average the log2FC values across different cell types in pseudobulk scRNA-seq data?
scrna-seq
rna-seq
log2fc
13 days ago by
JLee
• 0
0
votes
1
reply
200
views
Identify parent of each read in a GAF
gaf
vgteam
vg
updated 13 days ago by
Jordan M Eizenga
▴ 360 • written 14 days ago by
cfourps
▴ 10
0
votes
3
replies
275
views
Errors while trying to run Scenic
Scenic
updated 14 days ago by
GenoMax
135k • written 14 days ago by
Stavroula
• 0
0
votes
3
replies
289
views
How to find target genes From RNA seq data?
Cotton
DGE
RNA-seq
updated 14 days ago by
Ram
40k • written 14 days ago by
Fizzah
▴ 30
0
votes
0
replies
142
views
maftools - median survival time doesn't match plot
R
survival
maftools
K-M
14 days ago by
BioGuy
• 0
0
votes
1
reply
179
views
vg rna pantranscriptome
rna
vg
updated 14 days ago by
Jordan M Eizenga
▴ 360 • written 14 days ago by
z
• 0
0
votes
0
replies
138
views
Genetic distance in cM from VCF of non-reference species to run Beagle
plink
beagle
vcf
updated 14 days ago by
Ram
40k • written 14 days ago by
AndrMod
• 0
1
vote
4
replies
321
views
rRNA filtering from human RNA-seq data
rRNA
RNA-seq
14 days ago by
deniz
▴ 10
0
votes
5
replies
375
views
manhattan plot with vcf information
R
manhattan
vcf
updated 12 days ago by
dthorbur
▴ 560 • written 14 days ago by
sooni
▴ 10
0
votes
0
replies
562
views
after gatk VariantAnnotator -V *_com_norm.vcf -A AlleleFraction -O *_norm_AB.vcf There "nan,nan" or "nan" in my vcf file
gatk
AlleleFraction
VariantAnnotator
updated 14 days ago by
Ram
40k • written 14 days ago by
zhuo
• 0
2
votes
0
replies
149
views
the dispersion estimation of edgeR and DESeq2
estimation
dipersion
edgeR
DESeq2
15 days ago by
tommy
▴ 30
2
votes
3
replies
309
views
Genewise output help
genewise
updated 14 days ago by
Jean-Karim Heriche
26k • written 15 days ago by
lorenzoedg
• 0
2
votes
1
reply
189
views
Best Tools and Practices for CNV Variant Calling in WES Data
CNV
WES
updated 15 days ago by
Pierre Lindenbaum
157k • written 15 days ago by
Nadav
▴ 10
0
votes
2
replies
210
views
Identify genes for mapped reads with combined human-7HPV genome index
star
samtools
updated 15 days ago by
Ram
40k • written 15 days ago by
r.j.lock
• 0
0
votes
0
replies
134
views
Data for pathview() (KEGG Pathway Map) after EdgeR
EdgeR
LogFC
pathview
KEGG
15 days ago by
Ann
▴ 10
0
votes
0
replies
282
views
GTF/Reference genome adjustments? Gene-based differential expression analysis of genetically modified mouse line
RNA-seq
DGE
updated 15 days ago by
Ram
40k • written 15 days ago by
alex
• 0
0
votes
0
replies
155
views
Selecting SNPs for two-sample Mendelian randomization study/analysis
Two-sample
SNPs
Mendelian
randomization
15 days ago by
huynguyenacademia
• 0
0
votes
0
replies
147
views
cosine simialrity of mutation signature analysis
similarity
Mutational
analysis
signature
cosine
15 days ago by
probioquestioner
• 0
1
vote
1
reply
235
views
Significance testing of top vs. random SNPs
SNPs
significance
variance
statistical
updated 12 days ago by
dthorbur
▴ 560 • written 16 days ago by
am29
▴ 30
4
votes
2
replies
449
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 13 days ago by
yhdist
▴ 70 • written 16 days ago by
Cookin
▴ 10
0
votes
0
replies
155
views
Why we are using filtering >0 for up and <0 for down after TopTags() to extract de genes ids?
EdgeR
logfc
DEG
16 days ago by
Ann
▴ 10
0
votes
1
reply
184
views
PyMOL: how to list all selection names?
pymol
updated 15 days ago by
Wayne
★ 1.8k • written 16 days ago by
Ondina
▴ 90
2
votes
2
replies
231
views
Clustering algorithm based on grouping sequences into gene families
gene-families
clustering
updated 15 days ago by
Ram
40k • written 16 days ago by
francesco
• 0
0
votes
0
replies
151
views
Homozygous reference genotype for a GIAB genome
GIAB
IDs
reference
rs
Homozygous
16 days ago by
New2R
▴ 60
0
votes
0
replies
153
views
PRSice - Phenotype File Not Read Correctly
PRSice2
16 days ago by
V
• 0
0
votes
2
replies
1.6k
views
Question about REDItools
REDItools
updated 17 days ago by
Ethan Lee
• 0 • written 4.1 years ago by
tujuchuanli
▴ 100
1
vote
5
replies
538
views
Idat raw data conversion
idat
updated 16 days ago by
Giulio Genovese
▴ 330 • written 17 days ago by
Zi
• 0
1
vote
3
replies
370
views
What is "intersectional genetic strategy"? How does it work? What can it do?
cell-subtypes
16 days ago by
Ethan Lee
• 0
0
votes
0
replies
187
views
What metrics to use to calculate variant library evenness or uniformity or bias
library-bias
variant
updated 17 days ago by
Ram
40k • written 18 days ago by
eli_bayat
▴ 90
0
votes
0
replies
214
views
Tools to turn perfect phylogenetic matrix into a tree
parsimony
Phylogeny
tree
18 days ago by
Ritu_K
▴ 10
2
votes
4
replies
461
views
Help with celltype annotation
seurat
single-cell
17 days ago by
Chris
▴ 200
0
votes
1
reply
1.0k
views
Downstream analysis on multi-sample or single-sample VCF files?
next-gen
VCF
updated 18 days ago by
Ram
40k • written 2.9 years ago by
NGSCanBioinf
▴ 10
0
votes
1
reply
663
views
How to get enrichment of ERVs in differentially expressed peaks from ATAC-seq data?
ChIP-Seq
ERVs
ATAC-seq
updated 18 days ago by
pb11
▴ 10 • written 2.8 years ago by
fdemiguelsdp
• 0
3
votes
4
replies
385
views
Weighted analysis
RNA-seq
15 days ago by
Peter
• 0
1
vote
2
replies
284
views
Multiple testing adjustment for stepwise model selection
statistics
15 days ago by
mel22
▴ 100
0
votes
2
replies
302
views
Deseq2 colData for single condition
RNA-seq
17 days ago by
Petesview
• 0
0
votes
0
replies
177
views
PopGenome: there are missing regions when calculating Tajima's D per gene
PopGenome
16 days ago by
Bing
• 0
1
vote
2
replies
302
views
functional analysis
16S
metabarcoding
functionalanalysis
1 day ago by
safeassli
• 0
0
votes
1
reply
237
views
Asymmetric/biased log2FC values for low-expressed genes in DESeq2
DESeq2
DEG
fold-change
updated 18 days ago by
Ram
40k • written 18 days ago by
chenzy
• 0
0
votes
9
replies
1.0k
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
updated 7 days ago by
rfran010
▴ 840 • written 19 days ago by
pb11
▴ 10
327 results • Page
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Answer: tensorQTL interaction issue
Answer: Script for getting summary statistic of any genome using GTF or GFF3 ?
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Comment: How do you validate and verify your pipeline's software updates?
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GSEA with GO and KEGG datasets
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Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
Kevin Blighe
86k
It is difficult for me to comment, as I am not too informed on your IT infrastructure. What I can say is that it would be better to run the…
Answer: Converting from BED to SAF/GFF
by
alejandrogzi
▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Comment: Convert bed12 to GFF
by
alejandrogzi
▴ 30
Now there is [bed2gff](https://github.com/alejandrogzi/bed2gff), if you want to work only with a gff file!
Comment: Converting different annotation file formats (GTF/GFF/BED) to each other
by
alejandrogzi
▴ 30
now there is also [bed2gff](https://github.com/alejandrogzi/bed2gff) if you want to convert .bed files to .gff3 files!
Answer: How Do I Convert From Bed Format To Gff Format?
by
alejandrogzi
▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Answer: tensorQTL interaction issue
by
Solal
• 0
Writing a solution for anyone interested. The issue stems from a dosage error, some variant contains only heterozygous individuals and no h…
Answer: The Biostar Handbook. A bioinformatics e-book for beginners.
by
Qboy
• 0
Great book! I love using it to help my mentees to learn bioinformatics better. It would be also fantastic to compile all other necessary Pr…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
Thanks. I'll try.
Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
avelarbio46
▴ 30
Hi! I'm trying to parallelize your code (to run on a bunch of files), but it is not working because of multiple processes spawning. Do you …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
> so I don't think the genome size is available. Perhaps not for your specific strain but plenty of other Kpn genomes are available and th…
Comment: Kimura% of calcDivergenceFromAlign output
by
睿紘
• 0
For additional information, "Coverage for each repeat class and divergence (Kimura)" is also the result from calcDivergenceFromAlign.pl
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
By the way, I run Rockhopper on the untrimmed files, and the full match percentage grew to 20%-30%, and there are 1552 transcripts in the u…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
Here are the total bases in 4 fastq files (after adapter removal): 1,027,852,411, 1,041,895,083, 1,121,786,520, 1,299,721,929. I just rem…
Comment: Understanding mother and father alleles in VCF file
by
c.
• 0
actually they didn't tell me which relatives were from mother side and which from father side, you are right. But how can you find related …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
Correct. Data that went into the assembly.
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