Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
698 results • Page
2 of 14
Sort: Votes
Rank
Views
Votes
Replies
4
votes
9
replies
519
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
5 days ago by
Gabriel R.
★ 2.9k
4
votes
1
reply
363
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
22 days ago by
pairedttest
▴ 10
4
votes
2
replies
279
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 17 days ago by
Ram
44k • written 19 days ago by
carolofharvest
▴ 40
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 18 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
4
votes
3
replies
397
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 8 days ago by
Mathew
▴ 150 • written 11 days ago by
Christopher
• 0
4
votes
7
replies
648
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
22 days ago by
e.r.zakiev
▴ 210
4
votes
2
replies
290
views
GRCh38.gmap file
gnomix
gmap
17 days ago by
lorena9132
▴ 10
4
votes
6
replies
822
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 25 days ago by
dsull
★ 6.0k • written 29 days ago by
qudrat.nii
▴ 10
4
votes
2
replies
202
views
Duplicated sequence samtools
bowtie2
samtools
updated 8 days ago by
GenoMax
142k • written 8 days ago by
Moinuddin
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
22 days ago by
anna
▴ 20
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 22 days ago by
Andres
▴ 20 • written 9.7 years ago by
hermathena
▴ 40
4
votes
9
replies
643
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 1 day ago by
marco.barr
▴ 130 • written 6 days ago by
diqixiaoyaoer
▴ 20
4
votes
5
replies
470
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
23 days ago by
analyst
▴ 50
4
votes
1
reply
272
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 16 days ago by
zx8754
11k • written 17 days ago by
Jautis
▴ 570
4
votes
1
reply
344
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 7 days ago by
dariober
14k • written 8 days ago by
Holly
▴ 30
4
votes
11
replies
915
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 28 days ago by
LauferVA
4.2k • written 29 days ago by
dominickd
• 0
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 16 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 18 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 14 days ago by
chenl
▴ 10 • written 2.6 years ago by
Martyna
• 0
4
votes
7
replies
450
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
8 days ago by
Chen
• 0
4
votes
2
replies
293
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
13 days ago by
mnx0723
• 0
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 13 days ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
4
votes
7
replies
631
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 27 days ago by
dsull
★ 6.0k • written 28 days ago by
VITALA
• 0
4
votes
5
replies
4.4k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 5 days ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
4
votes
3
replies
450
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 24 days ago by
Arup Ghosh
3.2k • written 25 days ago by
chaco001
▴ 40
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 8 days ago by
Anitha
▴ 10 • written 5.1 years ago by
stephaniem
• 0
3
votes
8
replies
739
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 15 days ago by
Chris Dean
▴ 410 • written 19 days ago by
sovrappensiero
▴ 100
3
votes
2
replies
390
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 26 days ago by
dsull
★ 6.0k • written 26 days ago by
Aaliya
▴ 10
3
votes
4
replies
496
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 15 days ago by
Gordon Smyth
★ 7.2k • written 18 days ago by
SHN
▴ 40
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 14 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
3
votes
8
replies
278
views
Problem in getting geo file through GEOQUERY
file
download
Geo
14 hours ago by
anasjamshed
▴ 120
3
votes
2
replies
434
views
Extract protein sequence
fasta
alignment
blast
21 days ago by
anna
▴ 20
3
votes
4
replies
431
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
26 days ago by
QX
• 0
3
votes
7
replies
438
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
22 days ago by
Sergio A.S.
• 0
3
votes
6
replies
539
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 9 days ago by
Pine
▴ 20 • written 16 days ago by
snajafy
• 0
3
votes
4
replies
355
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 4 days ago by
Jeremy Leipzig
22k • written 6 days ago by
Ali
• 0
3
votes
1
reply
232
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 9 days ago by
aw7
▴ 300 • written 13 days ago by
Zeng Hao
▴ 40
3
votes
6
replies
2.1k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 25 days ago by
Ram
44k • written 2.4 years ago by
SYOSY
▴ 10
3
votes
3
replies
464
views
absolute path for symbolic links in Snakefile
Snakemake
updated 12 days ago by
Jesse
▴ 770 • written 4 weeks ago by
yifangt86
▴ 60
3
votes
3
replies
285
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 29 days ago by
Mensur Dlakic
★ 27k • written 29 days ago by
c_u
▴ 520
3
votes
3
replies
295
views
what is another word for a BLAST "hit"?
blast
alignment
11 days ago by
dec986
▴ 380
3
votes
4
replies
356
views
Truncated metadata file report from ENA Portal API
ena
python
11 days ago by
Giulia
• 0
3
votes
5
replies
445
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
1 day ago by
beantkapoor16
▴ 10
3
votes
3
replies
393
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 19 days ago by
ATpoint
82k • written 20 days ago by
alifafiq1
• 0
3
votes
5
replies
428
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
18 days ago by
Maverick
▴ 10
3
votes
5
replies
362
views
Generating mpileup file using samtools
mpileup
samtools
updated 19 days ago by
Joe
21k • written 19 days ago by
Ruqaiya
• 0
3
votes
0
replies
162
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 28 days ago by
Ram
44k • written 28 days ago by
carlopecoraro2
★ 2.5k
3
votes
3
replies
321
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 11 days ago by
Ram
44k • written 12 days ago by
Omics data mining
▴ 260
3
votes
9
replies
651
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 28 days ago by
Istvan Albert
100k • written 29 days ago by
Κοσμάς
• 0
3
votes
0
replies
93
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 18 hours ago by
Ram
44k • written 23 hours ago by
Rafael Soler
★ 1.2k
698 results • Page
2 of 14
Recent Votes
Construction of circos plot from WGS data
Answer: Different SNP at the at a position in vcf file compared to REF and ALT allele.
Answer: Different SNP at the at a position in vcf file compared to REF and ALT allele.
Different SNP at the at a position in vcf file compared to REF and ALT allele.
Comment: downloading chemical database from ChEMBL
Seurat-Merging and integrate
voom mean-variance plot has set of genes where variance increases with expression level
Recent Locations •
All
Cambridge/MA,
just now
Oviedo,
just now
Karachi,
2 minutes ago
China,
3 minutes ago
France,
8 minutes ago
United States,
9 minutes ago
Istanbul, Turkey,
9 minutes ago
Recent Awards •
All
Popular Question
to
anasjamshed
▴ 120
Student
to
Rafael Soler
★ 1.2k
Scholar
to
Jouni Sirén
▴ 370
Popular Question
to
Emily
23k
Popular Question
to
isha.lily20
▴ 10
Popular Question
to
Mohita
▴ 50
Popular Question
to
andres.firrincieli
3.6k
Recent Replies
Comment: samtools write-index
by
Pierre Lindenbaum
161k
can you please retry, but add rm -vf alignment.sorted.bam.bai before invoking minimap2. And `-o 'alignment.sorted.bam` should be enou…
Answer: from CRAM to fastq
by
Pierre Lindenbaum
161k
if the CRAM/BAM is paire-end, it **must** be sorted on query name using samtools collate https://x.com/lh3lh3/status/1132756684789768202 …
Comment: from CRAM to fastq
by
machaalani29
• 0
one of the issues is that I am not very sure how the sequencing was done, but I think it was single end. any suggestions hoot do that?
Comment: from CRAM to fastq
by
machaalani29
• 0
the option -c is to compress the file
Comment: from CRAM to fastq
by
GenoMax
142k
Possibly. You appear to have written the data to a single file (in case it was paired-end to begin with). Check to make sure secondary alig…
Comment: converting transcript IDs (Ensembl) to gene symbols in R
by
GenoMax
142k
https://www.biostars.org/u/18990/ : Please do not delete threads that have received a comment/answer.
Comment: downloading chemical database from ChEMBL
by
GenoMax
142k
Activities with `cucurbitacin A`: https://www.ebi.ac.uk/chembl/web_components/explore/activities/STATE_ID:RHxG8uDfrtbmiyaY55ic-w%3D%3D `cu…
Comment: KEGG analysis in R
by
letizia.ottaviani
• 0
Hello, I have a problem to do the analysis in R. I want to kindly ask you: How did you perform KEGG pathway enrichment analysis in R for…
Comment: downloading chemical database from ChEMBL
by
s
• 0
Thank you for your reply. I am still struggling with the first step, namely "select a compound" . can you be more specific with this step? …
Comment: No output when converting transcript IDs to gene symbols
by
ATpoint
82k
Honestly, why the overhead with biomart? Get a GTF file that matches your annotations, and just do a left join with your transcript IDs, it…
Answer: vg autoindex seems stuck after a week of running
by
Jouni Sirén
▴ 370
GCSA construction is fragile. It can use effectively unlimited amounts of time, memory, and disk space if the graph is too complex. That's …
Comment: Blastn, need help to increase speed
by
Dunois
★ 2.5k
What databases are you using that are creating such large index files?
Answer: Kraken2 Custom Database non-deterministic results
by
colindaven
6.4k
You're using 2 different databases, so results are obviously different. This has nothing to do with deterministic or stochastic behaviour. …
Answer: How to get 2 seurat objects into a DEseq
by
ultraanfibio
▴ 30
Its probably best practice to read all samples into the same seurat object, then do the clustering and asign the cell type labels. Anyways …
Comment: How do we do quantification using stringtie merge option for all the merged samp
by
ATpoint
82k
I ask the same I always ask when people use stringtie for human data. Do you really need a transcript assembly or do you just want gene cou…
Traffic: 2640 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6