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860 results • Page
1 of 18
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Votes
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0
votes
1
reply
52
views
How can I map coordinates between two strains of yeast?
coordinates
yeast
genome
mapping
fasta
updated 11 minutes ago by
dthorbur
▴ 830 • written 10 hours ago by
Jimmy
▴ 10
0
votes
1
reply
40
views
The difference blastn output when using subject and db options
genome
blastn
mite
annotation
tracker
updated 30 minutes ago by
GenoMax
136k • written 3 hours ago by
praasu
▴ 40
0
votes
1
reply
47
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 24 minutes ago by
Nitin Narwade
★ 1.5k • written 2 hours ago by
Bine
▴ 50
1
vote
3
replies
76
views
featureCounts results: low rate of 'Successfully assigned alignments'
FeatureCounts
HISAT2
RNA-seq
updated 44 minutes ago by
GenoMax
136k • written 2 hours ago by
Hamtaro
▴ 10
0
votes
1
reply
47
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 1 hour ago by
barslmn
★ 2.0k • written 3 hours ago by
Saurabh
• 0
0
votes
0
replies
29
views
How should I run ssgsea analysis ?
functional
TPM
enrichment
gsea
ssgsea
3 hours ago by
DareDevil
★ 3.3k
0
votes
1
reply
44
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
updated 41 minutes ago by
GenoMax
136k • written 3 hours ago by
GeneBC12
• 0
0
votes
1
reply
88
views
Mapping quality in `vg giraffe`
vg
updated 3 hours ago by
Xian
▴ 30 • written 8 hours ago by
Wenhai
• 0
0
votes
1
reply
55
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 1 hour ago by
barslmn
★ 2.0k • written 4 hours ago by
jiyoung
▴ 20
2
votes
4
replies
369
views
Protein Database
protein
course
database
updated 4 hours ago by
Elisabeth Gasteiger
★ 2.3k • written 4 days ago by
Mery
• 0
0
votes
0
replies
40
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
5 hours ago by
Smriti
▴ 10
0
votes
6
replies
210
views
I made an error when using metawrap to binning
metagenome
binning
metawrap
5 hours ago by
alice005201314
• 0
1
vote
1
reply
95
views
Bowtie mapping for single_end read
bowtie
updated 6 hours ago by
Tao
▴ 30 • written 8 hours ago by
Rita
• 0
0
votes
0
replies
41
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
6 hours ago by
cook.675
▴ 200
0
votes
4
replies
117
views
MRI VBM issue
MRI
VBM
ROI
Rhesus
7 hours ago by
Ethan Lee
• 0
2
votes
2
replies
118
views
SPAdes error: finished abnormally, OS return value: 21
SPAdes
8 hours ago by
jiyoung
▴ 20
0
votes
5
replies
482
views
Lack of correspondance of GFA node IDs to giraffe/call node IDs
giraffe
pggb
vg
updated 10 hours ago by
Wenhai
• 0 • written 5 weeks ago by
javierbelmor
• 0
0
votes
0
replies
46
views
String App in Cytoscape
App
String
cytoscape
10 hours ago by
hellokwmin
• 0
0
votes
0
replies
60
views
missing region in the process of annotation
annotatr
minfi
12 hours ago by
Aki
▴ 10
0
votes
3
replies
3.9k
views
pheatmap lengends are being cutoff
pheatmap
legends
rstudio
heatmaps
updated 13 hours ago by
Chris S.
▴ 320 • written 2.7 years ago by
enh
• 0
0
votes
0
replies
212
views
Job:
Postdoctoral Researcher in Alzheimer's disease Genetics, Multi-Omics, and Imaging Biomarkers, St Louis, MO, USA
Multi-Omics
Imaging
Alzheimer
Genetics
14 hours ago by
belloy
• 0
0
votes
2
replies
164
views
using RSEM with non Trinity assembly
SPAdes
Trinity
RSEM
15 hours ago by
jen
• 0
0
votes
1
reply
217
views
Help doing differential expression analysis -experimental design and gProfiler TF interpretation-
gProfiler
mRNA
Differential-expression
TCGA
updated 15 hours ago by
Zhenyu Zhang
★ 1.1k • written 6 days ago by
Camilo Andres
▴ 40
0
votes
1
reply
209
views
Diferences between TCGAbiolinks and cBioportal
R
TCGAbiolinks
cBioportal
updated 15 hours ago by
Zhenyu Zhang
★ 1.1k • written 5 days ago by
jomagrax
▴ 40
1
vote
0
replies
57
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
16 hours ago by
joe
▴ 390
0
votes
1
reply
64
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
updated 10 minutes ago by
dthorbur
▴ 830 • written 17 hours ago by
tw_140
• 0
2
votes
2
replies
128
views
Running STAR on fastq file generated from a RNA-seq experiment
STAR
RNAseq
fastq
files
updated 18 hours ago by
Darked89
4.5k • written 18 hours ago by
achanda
• 0
2
votes
3
replies
221
views
DEseq2 input
DEseq2
updated 17 hours ago by
ATpoint
78k • written 23 hours ago by
r.shiasi3897
▴ 10
0
votes
1
reply
119
views
Combine Geoids
Geoids
NCBI
updated 21 hours ago by
ATpoint
78k • written 1 day ago by
anasjamshed
▴ 120
1
vote
2
replies
182
views
Best practices for unstranded sequences in featureCounts
featurecounts
overlapping
unstranded
5 hours ago by
Enrique
• 0
1
vote
1
reply
140
views
Choose between pvalue & pvalue.adj
volcanoplot
updated 21 hours ago by
Istvan Albert
99k • written 22 hours ago by
Guitout
• 0
0
votes
4
replies
196
views
HTseq reports missing attribute name
htseq
18 hours ago by
Bjorn
• 0
3
votes
0
replies
103
views
Herald:
The Biostar Herald for Monday, November 27, 2023
herald
21 hours ago by
Biostar
2.3k
3
votes
16
replies
497
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
updated 37 minutes ago by
colindaven
5.7k • written 1 day ago by
analyst
▴ 10
4
votes
2
replies
1.8k
views
Masurca. Failed to pre-correct Nanopore data, please check your data!
Nanopore
Masurca
updated 23 hours ago by
colindaven
5.7k • written 2.4 years ago by
kamanovae
▴ 100
0
votes
0
replies
68
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
1 day ago by
user230613
▴ 350
0
votes
4
replies
210
views
Species coverage in the NCBI protein NR database ?
NR
updated 19 hours ago by
Istvan Albert
99k • written 1 day ago by
HERMAN
▴ 10
0
votes
7
replies
397
views
Issues while running htseq-count
Candida-glabrata
RNA-seq
htseq-count
1 day ago by
Foad
▴ 10
0
votes
0
replies
77
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
1 day ago by
Jaykishan
• 0
0
votes
0
replies
82
views
Harmony integration PC variance explained
scRNA
integration
harmony
1 day ago by
e.iich
• 0
0
votes
3
replies
195
views
merged rs number information
merged
dbsnp
9 hours ago by
sskimvd
• 0
2
votes
1
reply
132
views
Bedtools intersection
bedtools
bed
intersect
vcf
updated 1 day ago by
Pierre Lindenbaum
158k • written 1 day ago by
rejoeraymond776
▴ 10
0
votes
2
replies
170
views
RnBeads mean difference vs M-values
Methylation
updated 1 day ago by
Basti
★ 1.8k • written 1 day ago by
a.basitkhan1990
▴ 30
1
vote
2
replies
157
views
RnBeads which p-value to use
Methylation
RnBeads
updated 1 day ago by
ATpoint
78k • written 1 day ago by
a.basitkhan1990
▴ 30
1
vote
1
reply
139
views
Beginner differential methylation analysis
Methylation
updated 1 day ago by
Basti
★ 1.8k • written 1 day ago by
a.basitkhan1990
▴ 30
4
votes
8
replies
528
views
Docker: Pass reads file form host to container
docker
1 day ago by
davidmaimoun
▴ 50
2
votes
1
reply
215
views
EnhancedVolcano underrepresenting DEGs
R
updated 10 minutes ago by
Kevin Blighe
86k • written 1 day ago by
jabbari.parnian
▴ 30
4
votes
5
replies
1.6k
views
PyMOL: Gaps in protein structure yet shown by the sequence
PyMOL
structure
protein
updated 1 day ago by
pippo1980
• 0 • written 9 months ago by
spence.lank
▴ 10
0
votes
0
replies
99
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
1 day ago by
jiazheng_lin
• 0
0
votes
1
reply
170
views
multiple condition and time course in RNA-seq
edgeR
RNA-Seq
DESeq2
updated 1 day ago by
i.sudbery
18k • written 1 day ago by
tiancaigg
▴ 30
860 results • Page
1 of 18
Recent Votes
Comment: Construction of single sequence assembly out of contigs
Answer: featureCounts results: low rate of 'Successfully assigned alignments'
The Biostar Herald for Monday, November 27, 2023
Comment: use bioservices.UniProt (python) to map uniprot accession to [multiple] ensembl
Answer: Best practices for unstranded sequences in featureCounts
Answer: DEseq2 input
Comment: Filter out ALT contigs from CRAM
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Recent Replies
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
dthorbur
▴ 830
I don't have a suggestion for low yield DE analyses, but I am curious about the samples. Did you conduct any ribo-depletion steps prior to …
Answer: How can I map coordinates between two strains of yeast?
by
dthorbur
▴ 830
It sounds like you are looking for synteny between the two genomes. I'm assuming they are assembled, but that may not be the case. If so, […
Comment: Identify clusters of populations based on gene expression
by
Nitin Narwade
★ 1.5k
Why don't you just plot it on your UMAP If it is specific to one cluster/sub-population you should get a relatively high expression in that…
Answer: The difference blastn output when using subject and db options
by
GenoMax
136k
Default `task` option is `megablast` for `blastn` which looks for `highly similar sequences` compared to `blastn` which is looking for `som…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GenoMax
136k
https://www.biostars.org/u/14684/ may comment on this but it may be the order of operations that is causing this. After the `tpe` is applie…
Comment: Construction of single sequence assembly out of contigs
by
colindaven
5.7k
Inspector (only for long reads) and Merqury for short reads are also pretty good methods for doing a QC of your assembly.
Comment: featureCounts results: low rate of 'Successfully assigned alignments'
by
GenoMax
136k
> why I have soo many multimapping reads? That is a characteristic of the libraries. Not much you can do at this point in process. Just ha…
Comment: unicycler error : [Errno 13] Permission denied:
by
barslmn
★ 2.0k
This is not really a bioinformatics question. Either you're not the owner or in the group of the directory or the directory don't have wr…
Comment: Python function to export the annotated records to genbank file using python and
by
barslmn
★ 2.0k
Could you paste the error as printed to your screen?
Comment: Construction of single sequence assembly out of contigs
by
analyst
▴ 10
I have found dedup.sh script of bbmap tool that removes duplicated sequences. Also there is a seqtk tool. Is it safe to remove duplicated s…
Comment: featureCounts results: low rate of 'Successfully assigned alignments'
by
Hamtaro
▴ 10
Thank you for your reply. I how can I identify why I have soo many multimapping reads? The samples comes from blood from patients under d…
Comment: Construction of single sequence assembly out of contigs
by
analyst
▴ 10
Honestly I have not assessed duplication after assembly. However I used trimmomatic for data filtration before assembly. Trimmomatic param…
Answer: featureCounts results: low rate of 'Successfully assigned alignments'
by
kvn95ss
▴ 20
I could see the following clues from - hisat2 - ```23026867 (61.37%) aligned concordantly >1 times``` And from featureCounts - ``` Mu…
Comment: CPTAC data, download, merge
by
Mohita
▴ 50
I am also facing the same problem. I will be grateful if you help me out for this.
Comment: Circular genome browser
by
giammafer
▴ 20
Thank you very much for organising the 'awesome-genome-visualization' collection. I searched in your database before I made this question …
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