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Limit : this week
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226 results • Page
3 of 5
Sort: Rank
Rank
Views
Votes
Replies
2
votes
11
replies
801
views
RNA seq aligner?
Alignment
3 days ago by
tesfaye
• 0
1
vote
6
replies
366
views
Coverage depth map of genome from multiple sample coverage bedgraphs?
bedops
bedmap
coverage
2 days ago by
Agastya
▴ 10
1
vote
1
reply
169
views
Forum:
Can I use this community for software development?
software-development
updated 2 days ago by
Ram
43k • written 3 days ago by
avpuzanov
• 0
5
votes
2
replies
321
views
Forum:
Can questions and answers on biostars be asked only in English? Can't I use Russian for example?
language
updated 2 days ago by
Michael
54k • written 3 days ago by
avpuzanov
• 0
0
votes
0
replies
95
views
OSCC Dataset downlod using TCGA biolink
R
OSSC
TCGAbiolink
GDC
updated 2 days ago by
Ram
43k • written 3 days ago by
Biogeek
• 0
2
votes
1
reply
300
views
Tool:
TGSFilter, An ultra-fast and efficient tool for long reads filtering and trimming
genome-assembly
filtering
reads
trimming
updated 3 days ago by
Yingzi
• 0 • written 4 days ago by
Huiyang
▴ 180
0
votes
3
replies
250
views
two channel detection in SNP-chip
DNA
SNPchip
2-channel
updated 2 days ago by
LChart
3.9k • written 3 days ago by
Barma
• 0
2
votes
3
replies
213
views
Reference mouse phased vcf
mm10
vcf
phasing
Beagle
3 days ago by
machoo
• 0
0
votes
0
replies
83
views
Public datasets for genome-wide level mRNA-protein correlation calculation?
mRNA
protein
correlation
3 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
99
views
What is the usual basecalls length and reference mapping length relationship?
genome
alignment
rna-seq
updated 3 days ago by
Carlo Yague
8.6k • written 3 days ago by
anne
• 0
0
votes
1
reply
155
views
Difference in relative abundance between MicrobiomeDB and r phyloseq
phyloseq
updated 3 days ago by
Chris Dean
▴ 390 • written 3 days ago by
benkosta
• 0
3
votes
5
replies
583
views
How to filter Illumina Nirvana variant annotation?
nirvana
filtration
updated 3 days ago by
Pierre Lindenbaum
160k • written 3 days ago by
Kauno tvirtovės
• 0
0
votes
0
replies
114
views
News:
Online course: Introduction to GWAS
GWAS
Imputation
StatisticalPower
3 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
117
views
CIBERSORTx single cell reference sample file
scRNA-seq
CIBERSORTx
reference
4 days ago by
feather-W
• 0
0
votes
0
replies
140
views
beta coefficient improves after doing mediation analysis
coefficient
mediation
beta
regression
4 days ago by
rheab1230
▴ 140
1
vote
3
replies
745
views
Can shotgun metagenome approaches effectively target both RNA and DNA viruses in low-viral-load water samples?
RNA-virus
binning
metagenome
abundance
shotgun
updated 4 days ago by
joe
▴ 470 • written 6 days ago by
mathavanbioinfo
▴ 80
1
vote
1
reply
472
views
Help with SCENIC+
scenic-plus
updated 4 days ago by
corbettberry
▴ 10 • written 5 months ago by
Chris
▴ 260
1
vote
2
replies
343
views
What is meant by 'genomic order' in gatk's GatherVcfs, and how do I check for it?
gatk
vcf
merge
updated 4 days ago by
Pierre Lindenbaum
160k • written 4 days ago by
8armed
• 0
1
vote
2
replies
347
views
How to extract unmapped reads to assemble a plasmid
plasmid
transconjugant
reference-genome
4 days ago by
Barbara
• 0
0
votes
12
replies
768
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
2 days ago by
biwdpang
• 0
0
votes
0
replies
146
views
Cromwell slurm singularity call caching
cromwell
singularity
wdl
4 days ago by
asmariyaz23
▴ 10
0
votes
1
reply
200
views
Getting error in alignment using STAR
STAR
Error
updated 4 days ago by
Michael
54k • written 4 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
300
views
GIS overlay for environmental samples from NCBI
NCBI
environmental
SRA
GIS
ArcPro
5 days ago by
joe
▴ 470
0
votes
1
reply
225
views
PCA script correction
correction
script
PCA
updated 5 days ago by
BioinfGuru
★ 1.6k • written 5 days ago by
prity6459
• 0
3
votes
5
replies
376
views
Losing my mind with a VCF problem
vcf
bcftools
updated 5 days ago by
Michael
54k • written 5 days ago by
a.beggs
▴ 30
1
vote
13
replies
962
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 2 days ago by
lcj34
▴ 410 • written 8 days ago by
b.contreras.moreira
▴ 70
0
votes
2
replies
286
views
PopGenome lost individual information
PopGenome
1 day 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 5 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
2 days ago by
ujichu
• 0
1
vote
1
reply
195
views
genome.fa to indix files to use it in rna-seq analysis
RNA-seq
hisat2
index
updated 5 days ago by
GenoMax
140k • written 5 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
162
views
Tutorial:
Parsing HMMER output
HMMER
updated 5 days ago by
GenoMax
140k • written 5 days ago by
I0110
▴ 130
2
votes
5
replies
450
views
Searching for gene in multiple genomes
gene
genome
alignment
sequence
updated 5 days ago by
BioinfGuru
★ 1.6k • written 6 days ago by
Miya
• 0
0
votes
0
replies
177
views
Only positive enrichment score in GSEA
enrichmentanalysis
clusterprofiler
gsea
bioconductor
rnaseq
5 days ago by
enee
▴ 10
0
votes
7
replies
393
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
5 days ago by
dzisis1986
▴ 70
0
votes
0
replies
163
views
working with shapeit.
shapeit
5 days ago by
sanchit000singhdr098
• 0
0
votes
0
replies
155
views
Motif Scanning: HOMER vs MEME, settings?
homer
fimo
5 days ago by
mb
• 0
0
votes
0
replies
164
views
How to identify the phylogenetic node age of RNAs?
phylogeny
genome
evolution
RNA-seq
5 days ago by
Apex92
▴ 280
0
votes
9
replies
452
views
Intersect genomic locations with genes
fanc
Chromatin
conformation
Hic
hic
updated 5 days ago by
zx8754
11k • written 6 days ago by
naveedhasan2000
• 0
0
votes
3
replies
297
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv
compressing
varscan
bcftools
5 days ago by
kabir.deb
▴ 80
0
votes
0
replies
176
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
386
views
RNAseq
R
RNA-seq
Linux
6 days ago by
mrymrahimi70
• 0
0
votes
4
replies
495
views
calculating mean fragment length from CollectInsertSizeMetrics(Picard) output
count2fpkm
updated 6 days ago by
ATpoint
81k • written 9 days ago by
Niharika
• 0
2
votes
2
replies
257
views
Annotating indels and SNVs
annotation
indels
SNV
6 days ago by
am29
▴ 30
0
votes
4
replies
332
views
HISAT2 installation issue
HISAT2
updated 6 days ago by
GenoMax
140k • written 6 days ago by
eleven11
• 0
0
votes
8
replies
509
views
Fine-tuning NCBI taxid / taxidlist
BLAST
taxonomy
6 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
442
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications
dorado
basecalling
nanopore
methylation
updated 5 days ago by
LauferVA
4.1k • written 6 days ago by
njornet
▴ 10
0
votes
6
replies
406
views
Download Panther entry list
PANTHER
6 days ago by
Nicolas
• 0
226 results • Page
3 of 5
Recent Votes
Comment: Hybrid assembly Pacbio- Nanopore
Answer: vg call is time consuming
Answer: FDR and Bonferroni
Answer: FDR and Bonferroni
Answer: Choosing an FC Threshold
Answer: Choosing an FC Threshold
Differential expression analysis with very high duplication rate
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Recent Awards •
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Teacher
to
Haci
▴ 550
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▴ 90
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★ 9.4k
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amitpande74
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sarahmanderni
▴ 100
Recent Replies
Answer: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I want to calculate the mismatch rate on base-level, samtools stats in.bam | grep "error rate" | cut -f 2,3 error rate: 2.0…
Answer: Hybrid assembly Pacbio- Nanopore
by
colindaven
6.2k
If you have sufficient coverage of Pacbio HiFi reads - I think 30- 50X - then just use the Hifiasm https://github.com/chhylp123/hifiasm. It…
Answer: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
kayah
• 0
you should run JoinLayers() before FindAllMarkers()!!
Answer: Error occurs when migrate-n software performs "make mpis"
by
lingxue
• 0
Thank you very much. I will try to install it again according to your suggestion.
Comment: Only one read per run - Trying to use CellRangerv7
by
GenoMax
140k
https://www.ncbi.nlm.nih.gov/sra/?term=SRR16053948 Metadata indicates that this is: > Single-cell combinatorial-indexing RNA-sequencing (…
Comment: Paired layout, but one fastq file
by
GenoMax
140k
There is a BAM file available here: https://sra-pub-src-2.s3.amazonaws.com/SRR14667226/CTRL_possorted_genome_bam.bam.1 Please get that wit…
Comment: Only one read per run - Trying to use CellRangerv7
by
dsull
★ 5.6k
1. This is a comment, not an answer. Please don't post it as an answer. :) 2. This is sci-rna-seq, not 10x rna-seq. CellRanger would not …
Comment: Only one read per run - Trying to use CellRangerv7
by
Sky
▴ 10
Sorry for the delayed reply. I have included my code and the output from downloading the four files. Each dataset only resulted in one fast…
Answer: FDR and Bonferroni
by
joe
▴ 470
> Any idea why this is happening? For example, I got 1064 significant > probes from raw p-values, but only 18 from Bonferroni correction, a…
Comment: Paired layout, but one fastq file
by
Sky
▴ 10
I am also having a similar issue where there is only one fastq file but no bam file available so from my understanding I can't use bamtofas…
Comment: convert cds to seurat object
by
sooni
▴ 20
Yes, I tried with `as.Seurat`. But there is an error follwing: Error: `No data in provided assay - logcounts`. How can I solve this problem?
Comment: novel and know mir156 and mir172
by
gayachit
▴ 200
Do you have RNAseq or small RNAseq data?
Answer: Which fasta files are assembled transcripts IDBA_tran assembler ?
by
weidonglu
• 0
It should be transcript-20.fa,transcript-30.fa,transcript-40.fa,transcript-50.fa and transcript-60.fa. Then you have to merge these fasta-f…
Comment: Salmon Quantification in Alignment based-mode
by
GenoMax
140k
> /path/to//decoy.txt does not exist. Did you check to make sure the file is there? Also it is possible that by simply cutting the names a…
Comment: Why counting by diffbind and featurecounts differ?
by
Ankit
▴ 500
True in case of featurecounts and same I want to get via diffbind but it's not giving. I was trying to get the same results with diffbind.…
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