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1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
253
views
Regions not clear in VCF
whole-exome
variant-calling
updated 10 days ago by
Ram
43k • written 11 days ago by
priya.bmg
▴ 60
0
votes
0
replies
131
views
NA values showing at duplicacy removal step
Microarray
RNA-Seq
12 days ago by
prithvi.mastermind
▴ 50
0
votes
0
replies
133
views
Comparing molecular subtypes identified by microarray or bulk RNASeq in ssRNASeq data
microarrray
single-cell
RNASeq
subtype
12 days ago by
akhattri
▴ 50
0
votes
1
reply
260
views
cibersort. problem
cibersort
gema122
updated 10 days ago by
Ram
43k • written 15 days ago by
gem1
• 0
1
vote
3
replies
374
views
multiple sequence alignment
BLAST
multiple-sequence-alignment
clustal-omega
MSA
updated 10 days ago by
Ram
43k • written 13 days ago by
catherinemaria2728
• 0
0
votes
1
reply
207
views
Best way to add alter fastq file by adding short repeats
fastq
updated 13 days ago by
GenoMax
141k • written 13 days ago by
pairedttest
▴ 10
0
votes
0
replies
148
views
PolyA in FastQC results from EM-Seq?
fastqc
wgbs
polya
methylation
emseq
13 days ago by
Watermelon
• 0
0
votes
1
reply
204
views
POD5 files
ONT
updated 13 days ago by
GenoMax
141k • written 13 days ago by
marco.barr
▴ 60
1
vote
4
replies
338
views
How to get human-mouse conservation score from UCSC
conservation
mouse
IGV
human
score
13 days ago by
diqixiaoyaoer
▴ 10
0
votes
0
replies
153
views
Problem with GATK FilterMutectCalls : using contamination table doesn' t change anything
vcf
contaminationtable
gatk
filtermutectcalls
genomics
14 days ago by
Samuel
▴ 20
0
votes
1
reply
216
views
How do I know whether it is not a failure of ChIPseq data
ChIPseq
updated 11 days ago by
dthorbur
★ 1.9k • written 14 days ago by
Herman Einstein
• 0
0
votes
0
replies
143
views
CIBERSORT deconvolution by using long read sequencing data
long-read-sequencing
CIBERSORT
updated 13 days ago by
Ram
43k • written 14 days ago by
IVORY
• 0
0
votes
0
replies
153
views
Saccharomyces cerevisiae orthologs in plants
database
orthologs
14 days ago by
dec986
▴ 370
0
votes
0
replies
136
views
Looking for Comprehensive Virtual Screening Examples with Results Validation
drug-discovery
virtual-screening
molecular-docking
updated 14 days ago by
Ram
43k • written 14 days ago by
Stefano
• 0
0
votes
1
reply
175
views
samflags to removes mapped concordantly >1 times
samtools
Bowtie2
Metagenome
updated 8 days ago by
jkbonfield
★ 1.2k • written 14 days ago by
pompam_5904
• 0
4
votes
2
replies
213
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa
samtools
mapping
genome
updated 14 days ago by
Pierre Lindenbaum
161k • written 14 days ago by
Lee
• 0
0
votes
0
replies
123
views
TransDecoder ORF score to filter "noise" from de novo transcriptome assembly
transdecoder
assembly
transcriptome
updated 14 days ago by
Ram
43k • written 14 days ago by
tdamiani
• 0
0
votes
0
replies
113
views
Should I keep taxa that have 0 counts when calculating alpha diversity?
Shannon-Weiner
14 days ago by
DNAngel
▴ 250
0
votes
5
replies
313
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate
BUSCO.
updated 14 days ago by
GenoMax
141k • written 14 days ago by
Sony
▴ 10
0
votes
1
reply
146
views
MMSeqs2 Removing Redundancy
mmseqs
mmseqs2
updated 14 days ago by
GenoMax
141k • written 14 days ago by
dthorbur
★ 1.9k
0
votes
0
replies
107
views
Transcription Factor Binding sites intersecting Transposable Elements
TE
TFBP
14 days ago by
M.Adiba
• 0
0
votes
5
replies
312
views
Incongruencies in GT assignment by Freebayes
depth
freebayes
heterozygous
genotype
13 days ago by
virginia.baraja
• 0
0
votes
0
replies
101
views
Extracting tcga images for cnn in r
rstudio
python
tcga-lihc
svs
14 days ago by
jain72744
▴ 10
0
votes
3
replies
203
views
Peptide identification from Mass spec data
Transcriptomics
Proteins
Mass-spec
updated 14 days ago by
Ram
43k • written 14 days ago by
atharvakarkare14
▴ 10
0
votes
7
replies
382
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 14 days ago by
Papyrus
★ 2.9k • written 15 days ago by
doramora
▴ 10
0
votes
0
replies
332
views
Looking to improve my understanding of Homer's mergePeaks function: unclear of how the merged file is created?
Homer
ATACseq
15 days ago by
Ronin
• 0
0
votes
0
replies
87
views
RobustRankAggreg rankMatrix subscript out of boundaries
RobustRankAggreg
microarray
R
rankMatrix
15 days ago by
hagl
▴ 10
0
votes
3
replies
261
views
How do I handle it if there are multiple ENSEMBL IDs in one gene symbol in the scRNA sequencing data?
Seurat
scRNA-seq
count-matrix
11 days ago by
Jeyong
• 0
0
votes
0
replies
81
views
Handling data from RNA-seq experiement with negative cell controls / Water samples
rnaseq
15 days ago by
kvn95ss
▴ 20
1
vote
1
reply
175
views
R/Python script to collect allele frequency for batch of SNPs in gnomAD database
gnomAD
14 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
98
views
Seurat-DE analysis
seurat
DE
15 days ago by
odi
▴ 10
0
votes
1
reply
143
views
sorted bam file generated from gff transcript fastas, how to get counts with HTseq?
htseq
bam
updated 15 days ago by
Ram
43k • written 15 days ago by
RNAseqer
▴ 260
1
vote
5
replies
324
views
samtools filtering
samtools
updated 8 days ago by
jkbonfield
★ 1.2k • written 15 days ago by
sansan_96
▴ 80
0
votes
0
replies
100
views
R/Python function to retrieve interacted proteins from HPA database
HPA
15 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
106
views
Extracting Enhancer Regions from ENCODE Annotation Files
ENCODE
enhancer
15 days ago by
YamengWu
• 0
0
votes
0
replies
96
views
Normalization approaches of RNAseq data before WGCNA
DEseq2
voom
WGCNA
15 days ago by
gimenagomez
• 0
0
votes
6
replies
436
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
9 days ago by
marongiu.luigi
▴ 710
0
votes
2
replies
212
views
RNA-Seq isoforms identification
RNA-seq
updated 15 days ago by
Andres
▴ 20 • written 15 days ago by
latita.atun
• 0
2
votes
2
replies
245
views
Removing adapters in all the RNAseq samples regardless if they have or not, is it correct?
fastqc
trimming
adapters
cutadapt
RNAseq
updated 15 days ago by
dsull
★ 5.8k • written 15 days ago by
ev97
▴ 20
0
votes
0
replies
100
views
ChIPseeker annotation on gene or transcript level
ChIPseeker
annotation
ChIP-seq
15 days ago by
zea
• 0
0
votes
0
replies
105
views
Integration of scRNA, a conceptual doubt
Seurat
scRNA
Integration
15 days ago by
edoardofilippi1998
• 0
0
votes
0
replies
129
views
Diffbind and DESeq2 comparison for differential sites
diffbind
deseq2
updated 9 days ago by
Ram
43k • written 15 days ago by
Ankit
▴ 500
0
votes
0
replies
147
views
Requesting Insights on Potential Complex Structural Event Indicated by IGV
Manta
IGV
variant
translocation
structural
15 days ago by
pragnapcu
• 0
0
votes
2
replies
200
views
utr sequence retrieval from UCSC
UTR
SEQUENCING
UCSC
GENOME
updated 15 days ago by
GenoMax
141k • written 15 days ago by
kim
▴ 70
0
votes
0
replies
92
views
NicheNet cell-cell communication analysis outcome
nichenet
scRNA-seq
16 days ago by
QX
• 0
0
votes
1
reply
153
views
mirbase gff and mature fastas for custom STAR index genome?
mirbase
indexing
star
genome
15 days ago by
RNAseqer
▴ 260
0
votes
0
replies
98
views
WGCNA modulePreservation on three expression sets
WGCNA
16 days ago by
CTLong
▴ 110
0
votes
1
reply
187
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
16 days ago by
Gordon
• 0
0
votes
0
replies
125
views
Problem in merging multiple samples VCF file obtained from Structural variant caller Lumpy
SV
Variant-calling
VCF
updated 16 days ago by
Ram
43k • written 16 days ago by
sardana.thakur.prachi
• 0
0
votes
0
replies
98
views
How to extract BED-format annotation tracks for the newly inserted segments
bed
mauve
updated 16 days ago by
Ram
43k • written 16 days ago by
FZ
• 0
1,000 results • Page
4 of 20
Recent Votes
Answer: Ciriquant not configuring hisat2 indexed files
Answer: Ciriquant not configuring hisat2 indexed files
DNA Methylation: Sequencing Techniques
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Answer: Indexing the Reference Genome is not done in STAR
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
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Recent Replies
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
Pierre Lindenbaum
161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
b.contreras.moreira
▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
Comment: Korean human genome reference file
by
SeoGyun
• 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
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