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Limit : this year
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1,000 results • Page
1 of 20
Sort: Rank
Rank
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0
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0
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4
views
PacBio Pipeline and Tools for Variant Call
longread
pacbio
whatshap
pbmm2
just now by
Kiran
▴ 70
0
votes
0
replies
18
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
40 minutes ago by
Sebastian Hesse
▴ 320
0
votes
0
replies
10
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
1 hour ago by
jrodrigu
• 0
0
votes
1
reply
29
views
Create customized gene annotation file
reference
mkref
genome
cellranger
updated 1 hour ago by
ATpoint
72k • written 2 hours ago by
rhonddaskl
• 0
0
votes
0
replies
21
views
metagenomics data - AMR genes
amr
resistome
resistance
ARG
metagenomics
2 hours ago by
aziznasr1920
• 0
0
votes
1
reply
34
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 1 hour ago by
Pierre Lindenbaum
154k • written 2 hours ago by
herh
• 0
0
votes
0
replies
30
views
1000G reference panel for LD clumping
LD
3 hours ago by
en_keser
• 0
0
votes
0
replies
52
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
10 hours ago by
saladi1
▴ 30
0
votes
2
replies
578
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 17 hours ago by
Ram
39k • written 12 months ago by
Meeran
• 0
0
votes
7
replies
494
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 8 hours ago by
Vincent Laufer
★ 2.8k • written 4 days ago by
Camilo Andres
▴ 30
0
votes
2
replies
100
views
gatk Hardfilter Error
hardfilter
updated 18 hours ago by
Pierre Lindenbaum
154k • written 18 hours ago by
bestone
▴ 10
0
votes
2
replies
113
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
3 hours ago by
kamanovae
▴ 80
0
votes
1
reply
122
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 16 hours ago by
GenoMax
129k • written 19 hours ago by
fafad046
• 0
0
votes
2
replies
120
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
updated 4 hours ago by
WouterDeCoster
47k • written 21 hours ago by
Mohd
• 0
0
votes
2
replies
99
views
sorting BAM file
BAM
updated 1 hour ago by
ATpoint
72k • written 21 hours ago by
Mohammad Amin
• 0
1
vote
0
replies
76
views
Resequencing data of pangenome
NGS
PanGenome
Resequence
updated 16 hours ago by
Ram
39k • written 1 day ago by
bioinfo223
▴ 10
0
votes
0
replies
67
views
Converting rds file to h5ad and saving raw counts as X
R
seurat
updated 1 day ago by
zx8754
11k • written 1 day ago by
sidrah.maryam
▴ 50
0
votes
1
reply
125
views
Seurat: How to get all genes name of a cell ?
seurat
updated 13 hours ago by
jv
★ 1.2k • written 1 day ago by
Picasa
▴ 640
1
vote
0
replies
171
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 14 hours ago by
Ram
39k • written 1 day ago by
Supernova
• 0
0
votes
0
replies
88
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course
RNA-seq
pathway
updated 21 hours ago by
Ram
39k • written 1 day ago by
Fred
• 0
0
votes
1
reply
131
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 21 hours ago by
Ram
39k • written 1 day ago by
chengc2016zzu
• 0
0
votes
0
replies
82
views
Michigan Imputation Server - Local docker image
genotype
WGS
imputation
1 day ago by
batch_effect
• 0
0
votes
0
replies
76
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase
Databases
enzymes
Restriction
1 day ago by
Mahmoud Reda
▴ 10
1
vote
2
replies
173
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
49 minutes ago by
Pegasus
▴ 90
0
votes
0
replies
107
views
Merging multiple PLINK files
plink
merging
1 day ago by
Nejla
• 0
0
votes
0
replies
109
views
References selected by ExomeDepth CNV
CNV
ExomeDepth
updated 1 day ago by
GenoMax
129k • written 1 day ago by
keiko.asakura
• 0
0
votes
2
replies
199
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
9 hours ago by
J.F.Jiang
▴ 900
0
votes
2
replies
182
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping
Variant-calling
masking
updated 1 day ago by
Ram
39k • written 1 day ago by
Joel Wallenius
▴ 120
1
vote
3
replies
688
views
Regular Expression for conversion
Linux
grep
updated 20 hours ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
0
votes
1
reply
149
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 14 hours ago by
Ram
39k • written 1 day ago by
barrypraveen
▴ 110
0
votes
2
replies
159
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
1 day ago by
pg45863
• 0
0
votes
1
reply
131
views
ABySS Process Killed
ABySS
genome
assembly
updated 1 day ago by
GenoMax
129k • written 2 days ago by
asarcillo
• 0
0
votes
0
replies
92
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
2 days ago by
narges.bioinf
• 0
0
votes
3
replies
207
views
Query qbout single cell sequencing
fastq
ScRNA
updated 16 hours ago by
Ram
39k • written 2 days ago by
abbas.waseem.gcu
• 0
0
votes
1
reply
165
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 1 day ago by
fracarb8
▴ 950 • written 2 days ago by
Sun
• 0
0
votes
1
reply
165
views
Why coordinate sort is required in sambamba depths?
sorting
coordinate
sambamba
linux
samtools
updated 2 days ago by
Pierre Lindenbaum
154k • written 2 days ago by
MobiusT
▴ 10
0
votes
4
replies
260
views
I need help with a methyl array data analysis
methyl_array
DMPs
DMRs
beta_value
r
2 days ago by
Ahmad
▴ 10
0
votes
2
replies
228
views
Error in download library file in expression console software
expression
microarray
console
21 hours ago by
Mohammad
• 0
0
votes
6
replies
320
views
Demultiplexing bam file
demultiplexing
bam_file
Iontorrent
1 day ago by
hasani.iut6
▴ 60
1
vote
2
replies
250
views
DEgs RNAseq
RNAseq
2 days ago by
Juan
• 0
0
votes
0
replies
161
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
11 hours ago by
Vincent Laufer
★ 2.8k
0
votes
1
reply
233
views
problem of Global Biobank Meta-analysis Initiative
GWAS
updated 2 days ago by
Fabio Marroni
★ 3.0k • written 3 days ago by
1362321710
• 0
1
vote
1
reply
219
views
DownsampleSam
picard
DownsampleSam
updated 3 days ago by
Pierre Lindenbaum
154k • written 3 days ago by
mathalfilip
• 0
0
votes
1
reply
220
views
Error while running Megahit
Megahit
updated 3 days ago by
Mensur Dlakic
★ 23k • written 4 days ago by
abhiramiabhirami9072
• 0
2
votes
5
replies
386
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
1 day ago by
DanielEB_fisk
• 0
0
votes
0
replies
192
views
corresponding clinical data from TCGA database of PSI values for CCA AS events in spliceseq database
TCGA
4 days ago by
dima
• 0
1
vote
0
replies
247
views
How to assess which cell population is most affected by treatmant in single cell rna seq data?
transcriptomics
single-cell
RNA
DEG
4 days ago by
abbas89
▴ 10
0
votes
1
reply
723
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure
pymol
protein
pdb
python
updated 20 hours ago by
Joe
21k • written 4 days ago by
Aatif Hashmi
• 0
0
votes
1
reply
296
views
Deferentially expressed gene with high log2foldchange by DESeq2; but not meaningful at the individual level
DESeq2
RNA-seq
DGEA
updated 4 days ago by
Vincent Laufer
★ 2.8k • written 4 days ago by
Sara
▴ 10
1
vote
2
replies
251
views
Abyss taking a Long time to run
abyss
assembly
genome
fastq
4 days ago by
Maliha
▴ 20
1,000 results • Page
1 of 20
Recent Votes
Answer: Alignment of case vs. control from different origin
What type of normalization did they use in this article?
Answer: I don't want to believe the Interproscan DB estimated download time.
C: removing overrepresented sequences from rna-seq
C: removing overrepresented sequences from rna-seq
C: Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Answer: Any methods available to do QC analysis of Pacbio raw data??
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edus_bioinfo
▴ 20
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barslmn
★ 1.5k
Supporter
to
cthangav
▴ 40
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saladi1
▴ 30
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tarek.mohamed
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kamanovae
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Recent Replies
Comment: What type of normalization did they use in this article?
by
JACKY
▴ 90
I see, do you think there is any way to retrieve the uncorrected TPM data? can I undo the corrections and scalings applied to the data?
Comment: Alignment of case vs. control from different origin
by
ATpoint
72k
I would not even do the trimming. Any differential analysis of case (normal/control) versus anything in TCGA (progressed cancer) is going t…
Comment: Docker Error while running nf-core/rnaseq pipeline
by
eesha28112001
• 0
How do I do that?
Comment: MACS2 peak calling
by
ATpoint
72k
You do not need strand information for this as, as I said, strands do not apply in DNA-seq.
Answer: Docker Error while running nf-core/rnaseq pipeline
by
ATpoint
72k
> read-only file system You must make sure that the output destination is writable.
Answer: sctransform on scRNA seq
by
ATpoint
72k
No, there is no magic to make data appear where previously there were none.
Answer: What type of normalization did they use in this article?
by
Matthias Zepper
3.7k
> Transcriptomic analysis > > [...] We subsequently filtered genes that > were not expressed in any of the samples (in each cohort > indep…
Comment: How to get a comperative result of 2 bed files?
by
Pierre Lindenbaum
154k
what kind of measurement do you need ? I see one bed file in your description , what are the TWO bed file ?
Comment: MACS2 peak calling
by
Maurice
• 0
Thank you! And for what regards peaks annotation, how can the tool I'm going to use assign peaks to the correct location without knowing t…
Comment: sorting BAM file
by
ATpoint
72k
You can simply use `samtools sort` to get rid of this read group nonsense these Broad institute tools always complain about.
Answer: Which type of variant caller should I use in a WES normal cell line sample?
by
ATpoint
72k
Any variant caller will do. Somatic calling is usually an additional mode while calling without matched normal is typically always possible.
Comment: Create customized gene annotation file
by
ATpoint
72k
Plese confirm whether you read and tried the manual: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/…
Answer: MACS2 peak calling
by
ATpoint
72k
Yes, that is correct. Peaks from experiments such as ChIP-seq or ATAC-seq are based on DNA, which is double-stranded and unlike RNA (where …
Answer: Alignment of case vs. control from different origin
by
i.sudbery
17k
I hate to be the one to tell you this, but the reason you have been unable to find an answer isnthat what you are trying to do is not gener…
Answer: Peaks annotation on bacterial genome
by
Maurice
• 0
Thank you for your kind reply! I have just a further question. Which is the difference between using annoPeaks and annotatePeaksinbatch wi…
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