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1,000 results • Page
3 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
106
views
t2t Reference gtf file
t2t
2 days ago by
Emre
• 0
1
vote
2
replies
232
views
BWA MEM Alignment mapped small part of the reads!!
bwa
mem
updated 2 days ago by
bioruffo
▴ 40 • written 2 days ago by
Bunit
• 0
1
vote
0
replies
98
views
Job:
Job Opening - Fred Hutch - Director of Training & Community
fred-hutchinson
updated 2 days ago by
Ram
43k • written 3 days ago by
Fred Hutch (Recruiting)
▴ 20
0
votes
0
replies
109
views
Correlation analysis in single-cell sequencing data
scRNA-seq
correlation
scATAC-seq
3 days ago by
Yingying
• 0
0
votes
0
replies
105
views
MIENTURNET - miRNA enrichment analysis
miRNA-enrichment
mRNA
RNA
updated 3 days ago by
Ram
43k • written 3 days ago by
PBC
▴ 10
0
votes
5
replies
315
views
Parsing fasta file by coordinates
linux
fasta
updated 6 hours ago by
GenoMax
140k • written 3 days ago by
sorrymouse
▴ 120
0
votes
2
replies
220
views
comparing VCF files
long-reads
VCF
variants
ONT
nanopore
2 days ago by
eesiribloom
▴ 50
0
votes
2
replies
204
views
Using velocyto on 3'UTR 10x single-cell RNA-Seq data
single-cell
single-end
10x
velocyto
2 days ago by
Sergio
• 0
0
votes
0
replies
129
views
Job:
Post-doctoral positions in computational biomedicine
data-science
biomedicine
machine-learning
updated 3 days ago by
Ram
43k • written 3 days ago by
pandey.gaurav
▴ 200
6
votes
13
replies
481
views
Allocating right resources to HPC using LSF scheduler
BWA
GATK
hpc
lsf
bsub
3 days ago by
Maverick
▴ 10
10
votes
6
replies
4.0k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 2 days ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
0
votes
5
replies
454
views
How to download RNAseq data of only male KIRC patients?
TCGAbiolinks
3 days ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
88
views
Multifactor Analysis in DiffBind
DiffBind
ChIPseq
ChIP-seq
3 days ago by
erbrocato
• 0
0
votes
0
replies
104
views
How to calculate weighted transcript length for each gene?
salmon
tximport
rna-seq
updated 3 days ago by
Ram
43k • written 3 days ago by
barrypraveen
▴ 130
1
vote
2
replies
224
views
Deseq generating warning "the model matrix is not full rank"
deseq
updated 2 days ago by
bioruffo
▴ 40 • written 3 days ago by
MAPK2
▴ 40
4
votes
2
replies
3.3k
views
Genome annotation: convert gtf to gff3 file
gff3
gtf
updated 3 days ago by
vague-barracuda-4686
• 0 • written 16 months ago by
shinyjj
▴ 50
0
votes
3
replies
226
views
What tools to assess coverage, completeness and contamination?
completeness
contamination
covarage
updated 3 days ago by
Mensur Dlakic
★ 26k • written 3 days ago by
Kárita
• 0
0
votes
0
replies
83
views
Metacoder plot_cladogram long calculation times
Metacoder
updated 3 days ago by
Ram
43k • written 3 days ago by
La52dA97b6
• 0
4
votes
9
replies
668
views
Snakemake >= version 8 cluster configuration and SLURM job submission
parallelization
slurm
snakemake
cluster
updated 3 days ago by
Simon
▴ 10 • written 7 days ago by
Maxwell
▴ 20
0
votes
1
reply
168
views
RNA-seq with normalized cpm count
RNA-seq
Deseq2
EdgeR
updated 3 days ago by
Ram
43k • written 3 days ago by
GiV17
▴ 50
0
votes
2
replies
199
views
how to run limma for large datasets
R
HPC
biostatistics
statistics
updated 3 days ago by
Ram
43k • written 3 days ago by
Bioinfonext
▴ 460
0
votes
4
replies
253
views
Confirm if a genome position falls into a coding exon
exon
UCSC
coding
updated 3 days ago by
Pierre Lindenbaum
160k • written 3 days ago by
Lila M
★ 1.2k
1
vote
0
replies
97
views
Downloading immne signature and pathway signature genes form publication and KEGG
genes
TRANSCRIPTOME_signature
3 days ago by
mrazib0210
▴ 10
0
votes
1
reply
146
views
NCBI gene data
Variants
NCBI
updated 3 days ago by
GenoMax
140k • written 3 days ago by
chandrakala.m
• 0
0
votes
1
reply
139
views
How to perform GO enrichment analysis for assembled sequence ?
GO-enrichment
Gene-Ontology
updated 3 days ago by
Ram
43k • written 3 days ago by
Sony
▴ 10
3
votes
0
replies
125
views
Herald:
The Biostar Herald for Monday, March 25, 2024
herald
3 days ago by
Biostar
2.6k
2
votes
4
replies
1.6k
views
bowtie2 maximum value of MAPQ
bowtie2
bowtie
updated 3 days ago by
axol0tl
• 0 • written 3.6 years ago by
sami
▴ 30
1
vote
8
replies
340
views
0-based coordinates from samtools depth
samtools
coverage
depth
updated 3 days ago by
Pierre Lindenbaum
160k • written 3 days ago by
marco.barr
▴ 30
1
vote
0
replies
108
views
checkm lineage.ms output file
checkm
lineage
3 days ago by
A_heath
▴ 160
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna
rRNA
metagenomics
updated 3 days ago by
Ram
43k • written 13.5 years ago by
toshnam
▴ 650
3
votes
14
replies
433
views
Variant calling of GBS data
GBS
variants
BQSR
6 hours ago by
analyst
▴ 10
2
votes
11
replies
802
views
RNA seq aligner?
Alignment
3 days ago by
tesfaye
• 0
1
vote
6
replies
370
views
Coverage depth map of genome from multiple sample coverage bedgraphs?
bedops
bedmap
coverage
2 days ago by
Agastya
▴ 10
1
vote
1
reply
170
views
Forum:
Can I use this community for software development?
software-development
updated 3 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 3 days ago by
Michael
54k • written 3 days ago by
avpuzanov
• 0
0
votes
0
replies
96
views
OSCC Dataset downlod using TCGA biolink
R
OSSC
TCGAbiolink
GDC
updated 3 days ago by
Ram
43k • written 3 days ago by
Biogeek
• 0
2
votes
1
reply
301
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
252
views
two channel detection in SNP-chip
DNA
SNPchip
2-channel
updated 3 days ago by
LChart
3.9k • written 4 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 4 days ago by
anne
• 0
0
votes
1
reply
155
views
Difference in relative abundance between MicrobiomeDB and r phyloseq
phyloseq
updated 4 days ago by
Chris Dean
▴ 390 • written 4 days ago by
benkosta
• 0
3
votes
5
replies
593
views
How to filter Illumina Nirvana variant annotation?
nirvana
filtration
updated 4 days ago by
Pierre Lindenbaum
160k • written 4 days ago by
Kauno tvirtovės
• 0
0
votes
0
replies
115
views
News:
Online course: Introduction to GWAS
GWAS
Imputation
StatisticalPower
4 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
140
views
beta coefficient improves after doing mediation analysis
coefficient
mediation
beta
regression
5 days ago by
rheab1230
▴ 140
1
vote
3
replies
746
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 5 days ago by
joe
▴ 470 • written 7 days ago by
mathavanbioinfo
▴ 80
1
vote
1
reply
473
views
Help with SCENIC+
scenic-plus
updated 5 days ago by
corbettberry
▴ 10 • written 5 months ago by
Chris
▴ 260
1
vote
2
replies
345
views
What is meant by 'genomic order' in gatk's GatherVcfs, and how do I check for it?
gatk
vcf
merge
updated 5 days ago by
Pierre Lindenbaum
160k • written 5 days ago by
8armed
• 0
1
vote
2
replies
347
views
How to extract unmapped reads to assemble a plasmid
plasmid
transconjugant
reference-genome
5 days ago by
Barbara
• 0
0
votes
12
replies
771
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
2 days ago by
biwdpang
• 0
1,000 results • Page
3 of 20
Recent Votes
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
Some things never change ... the most common mistake is still the one on top there
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