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308 results • Page
2 of 7
Sort: replies
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Views
Votes
Replies
3
votes
4
replies
431
views
During alignment STAR has stopped at started alignment step
STAR
updated 11 days ago by
Ram
40k • written 7 weeks ago by
Santhi
• 0
0
votes
4
replies
636
views
CAZy database has multiple family sequence...
metagenomics
cazy
annotation
updated 24 days ago by
JyiYeung
• 0 • written 9 months ago by
GYUDAE
• 0
0
votes
4
replies
232
views
Sequence quality drops in the 3' end of the left sequence in paired end. What could be the cause?
sequencing
updated 3 days ago by
GenoMax
134k • written 3 days ago by
eggrandio
▴ 40
1
vote
4
replies
313
views
rRNA filtering from human RNA-seq data
rRNA
RNA-seq
11 days ago by
deniz
▴ 10
2
votes
4
replies
386
views
join the control replicates
RNA-seq
updated 15 days ago by
seidel
11k • written 16 days ago by
Jean Pierre
• 0
1
vote
4
replies
224
views
How to filter vcf file by MAF using bcftools?
bcftools
vcf
updated 3 days ago by
Ram
40k • written 3 days ago by
_quantum_girl_
▴ 10
2
votes
4
replies
450
views
Help with celltype annotation
seurat
single-cell
14 days ago by
Chris
▴ 200
3
votes
4
replies
374
views
Weighted analysis
RNA-seq
12 days ago by
Peter
• 0
2
votes
4
replies
305
views
Using STAR aligner to build index of hg38
hg38
STAR
alignment
RNAseq
index
6 days ago by
Grace
• 0
1
vote
4
replies
325
views
htseq-count reports count values for deleted genes
rna-seq
htseq
19 days ago by
kmyers2
▴ 80
0
votes
4
replies
310
views
Split reads along the genome in my samples
DNA
sequencing
17 days ago by
paulaotero.sanchez
• 0
0
votes
3
replies
720
views
to annotate BEDPE files
bedtools
annotate
updated 3 days ago by
Lhl
▴ 760 • written 2.6 years ago by
Bogdan
★ 1.4k
0
votes
3
replies
261
views
CNV using GISTIC
CNV
GISTIC
updated 17 days ago by
Ram
40k • written 17 days ago by
ananta.kapoor
• 0
0
votes
3
replies
208
views
What is the correct procedure to generate a consensus bacterial sequence?
consensus
samtools
illumina
fastq
1 day ago by
marongiu.luigi
▴ 690
1
vote
3
replies
674
views
How to determine plasmid or chromosomal origin?
plasmid
chromosomal-origin
updated 9 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
0
votes
3
replies
352
views
Seeking Assistance for Interpreting a Network Representation on String-DB.org
gene-ontology
GO
enrichment
Proteome
stringdb
updated 21 days ago by
rfran010
▴ 830 • written 22 days ago by
Biomed-jeh
• 0
1
vote
3
replies
258
views
comparision of umap single cell
single-cell
2 days ago by
synat.keam
▴ 80
0
votes
3
replies
735
views
How to add translation of CDS in Artemis?
translation
Artemis
updated 9 days ago by
Ram
40k • written 2.7 years ago by
A_heath
▴ 140
3
votes
3
replies
221
views
Clustering in single cell
seurat
single-cell
2 days ago by
Chris
▴ 200
0
votes
3
replies
278
views
Genomic location of MUC16
VNTR
genome
updated 23 days ago by
GenoMax
134k • written 25 days ago by
fi1d18
★ 4.2k
1
vote
3
replies
243
views
Finding sequences in unannotated genomes using reference coordinates
consensus
VCF
updated 8 days ago by
Ram
40k • written 8 days ago by
Prangan
▴ 20
0
votes
3
replies
336
views
Pearson correlation with different row numbers across two datasets?
perasoncorrelation
pearson
error
updated 17 days ago by
Kevin Blighe
86k • written 18 days ago by
siefeldin
▴ 30
0
votes
3
replies
180
views
Bug of vg surject
vg
updated 3 days ago by
Jordan M Eizenga
▴ 360 • written 3 days ago by
Qi
• 0
0
votes
3
replies
2.0k
views
extraction of original gene iDs from reference annotation file
rna-seq
updated 10 days ago by
aishwarya
• 0 • written 5.3 years ago by
blooming.daisy333
▴ 110
0
votes
3
replies
354
views
RSubread DESeq2
RNA-seq
subread
differential-expression
deseq2
updated 12 days ago by
Ram
40k • written 21 days ago by
Beyza
• 0
0
votes
3
replies
325
views
RdRp scan - identifying/detecting viruses- metagenomic workflow- need help
RdRp
virus-detection
metagenomic
updated 12 days ago by
Ram
40k • written 16 days ago by
eric--carron
• 0
1
vote
3
replies
285
views
Question regarding MACS2 approach of peak calling
MACS2
sequencing-depth
chipseq
updated 10 days ago by
ATpoint
77k • written 19 days ago by
rkc5
• 0
0
votes
3
replies
268
views
Errors while trying to run Scenic
Scenic
updated 11 days ago by
GenoMax
134k • written 11 days ago by
Stavroula
• 0
1
vote
3
replies
363
views
What is "intersectional genetic strategy"? How does it work? What can it do?
cell-subtypes
13 days ago by
Ethan Lee
• 0
0
votes
3
replies
290
views
Assigning GO ids to blast hits
Linux
GO
blast
updated 4 days ago by
gv
• 0 • written 23 days ago by
Mousumi Akter
• 0
2
votes
3
replies
302
views
Genewise output help
genewise
updated 11 days ago by
Jean-Karim Heriche
26k • written 12 days ago by
lorenzoedg
• 0
0
votes
3
replies
290
views
Extracting/assembling organellar reads from RNAseq data
transcriptome
star
alignment
mapping
updated 12 days ago by
LChart
3.4k • written 19 days ago by
Miles
• 0
1
vote
3
replies
253
views
Sub-sampleing bam files based on sequencing_summary.txt (guppy output)
samtools
guppy
updated 10 days ago by
GenoMax
134k • written 10 days ago by
anika.john
• 0
2
votes
3
replies
1.5k
views
Racon command line with paired-ends Illumina reads
Illumina
Racon
updated 9 days ago by
Ram
40k • written 2.1 years ago by
A_heath
▴ 140
0
votes
3
replies
282
views
How to find target genes From RNA seq data?
Cotton
DGE
RNA-seq
updated 11 days ago by
Ram
40k • written 11 days ago by
Fizzah
▴ 30
0
votes
3
replies
399
views
Understanding the Impact of DNA Methylation on Gene Expression in Different Genomic Regions
methylation
EPICarray
17 days ago by
Irene
• 0
2
votes
3
replies
351
views
How to label only a few genes of interest in heatmap of bulk RNA-seq
RNA-seq
updated 24 days ago by
Ram
40k • written 26 days ago by
Chris
▴ 200
1
vote
3
replies
321
views
How to determine the total count for each gene in lymphotype B
scRNAseq
Seurat
2 days ago by
dalibenam64
• 0
2
votes
3
replies
294
views
Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication
apoptosis
updated 10 days ago by
Ram
40k • written 10 days ago by
txema.heredia
▴ 80
1
vote
3
replies
310
views
Requesting further clarification on interpreting relative gene expression strength
R
normalization
TPM
RNA-seq
DESeq2
updated 16 days ago by
ATpoint
77k • written 4 weeks ago by
Abhishek
• 0
1
vote
3
replies
354
views
SNPs that have the same position and alleles, which rsnumber to pick?
dbSNP
SNV
SNP
updated 22 days ago by
LauferVA
3.7k • written 26 days ago by
TreasureChest
• 0
3
votes
3
replies
2.2k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 4 days ago by
Ram
40k • written 2.0 years ago by
Anand
▴ 40
0
votes
3
replies
333
views
Not all variants are annotated with AF - expected or a problem?
Alignment
WGS
Calling
Variant
updated 22 days ago by
GenoMax
134k • written 23 days ago by
Luiz
▴ 30
4
votes
3
replies
394
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
29 days ago by
stefano.iantorno
▴ 70
1
vote
3
replies
200
views
differences between trajectories in conditions with Monocle3 or other tools
trajectory
scRna-seq
monocle3
single-cell
updated 1 day ago by
Amitm
★ 2.2k • written 1 day ago by
Chironex
▴ 40
0
votes
3
replies
324
views
Calculating MAF from EAF from a GWAS summary statistics file in R
R
EAF
updated 23 days ago by
Ram
40k • written 25 days ago by
namraahmad173
• 0
5
votes
3
replies
290
views
Visualisation of accessible regions in single cell atacseq data
visualization
scATAC-seq
single-cell
updated 16 days ago by
Ram
40k • written 16 days ago by
sarahmanderni
▴ 90
2
votes
2
replies
225
views
Clustering algorithm based on grouping sequences into gene families
gene-families
clustering
updated 12 days ago by
Ram
40k • written 13 days ago by
francesco
• 0
1
vote
2
replies
317
views
Converting scMultiome data to loom using SEURAT
scMultiome
CCAF
Seurat
22 days ago by
halimaakhter014
• 0
1
vote
2
replies
157
views
Is it normal if regress out the cell cycle effects but the DEGs are quite the similar (no big changes)
regress_out
Cell_cycle
Seurat
5 days ago by
alwayshope
▴ 30
308 results • Page
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A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
Comment: Significance testing of top vs. random SNPs
Answer: Search RCSB with a list of protein names?
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
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Comment: MAKER: WARNING: Could not get initialization lock. Trying Again...
by
GenoMax
134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files
by
Alex Reynolds
35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
• 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
• 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File
by
Reem
• 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR
by
Trivas
★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies)
by
Jeremy Leipzig
21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
by
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Pierre Lindenbaum
157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output
by
langziv
▴ 50
I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files
by
Pierre Lindenbaum
157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output
by
shelkmike
▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages
by
ATpoint
77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
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