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 : all time
all time
today
this week
this month
this year
1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
104
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 4 days ago by
Ram
39k • written 4 days ago by
Mah
• 0
1
vote
3
replies
215
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 4 days ago by
GenoMax
129k • written 4 days ago by
mls
• 0
0
votes
0
replies
105
views
snpEff error. No CDS checked
snpEff
gtf
WES
4 days ago by
fifty_fifty
▴ 40
0
votes
0
replies
104
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
4 days ago by
Maddie
• 0
1
vote
2
replies
196
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
3 days ago by
rheab1230
▴ 140
2
votes
4
replies
232
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 4 days ago by
Ram
39k • written 4 days ago by
miguellarrazlopezdenovales
• 0
0
votes
0
replies
82
views
Pore-C-Snakemake output files
contacts
4 days ago by
oksana03fel
• 0
1
vote
0
replies
106
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
4 days ago by
fr
▴ 200
0
votes
2
replies
171
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 4 days ago by
rpolicastro
12k • written 4 days ago by
Pac314
▴ 10
0
votes
2
replies
159
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
3 days ago by
survive
• 0
1
vote
1
reply
125
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 4 days ago by
GenoMax
129k • written 4 days ago by
hashim.rana11
▴ 20
2
votes
2
replies
161
views
Create customized gene annotation file
reference-genome
cellranger
16 hours ago by
rhonddaskl
• 0
0
votes
0
replies
78
views
metagenomics data - AMR genes
amr
resistome
resistance
ARG
metagenomics
4 days ago by
aziznasr1920
▴ 10
1
vote
3
replies
181
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 3 days ago by
Pierre Lindenbaum
154k • written 4 days ago by
herh
• 0
0
votes
0
replies
73
views
1000G reference panel for LD clumping
LD
4 days ago by
en_keser
• 0
0
votes
0
replies
82
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
5 days ago by
saladi
▴ 30
0
votes
2
replies
608
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 5 days ago by
Ram
39k • written 13 months ago by
Meeran
• 0
0
votes
7
replies
561
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 4 days ago by
Vincent Laufer
★ 2.9k • written 8 days ago by
Camilo Andres
▴ 30
0
votes
3
replies
199
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 4 days ago by
andres.firrincieli
3.3k • written 5 days ago by
kamanovae
▴ 80
0
votes
1
reply
152
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 5 days ago by
GenoMax
129k • written 5 days ago by
fafad046
• 0
0
votes
3
replies
186
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
3 days ago by
Mohd
▴ 20
1
vote
2
replies
175
views
sorting BAM file
BAM
updated 4 days ago by
ATpoint
72k • written 5 days ago by
Mohammad Amin
• 0
0
votes
0
replies
85
views
Converting rds file to h5ad and saving raw counts as X
R
seurat
updated 5 days ago by
zx8754
11k • written 5 days ago by
sidrah.maryam
▴ 50
0
votes
1
reply
146
views
Seurat: How to get all genes name of a cell ?
seurat
updated 5 days ago by
jv
★ 1.2k • written 5 days ago by
Picasa
▴ 640
1
vote
0
replies
233
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 5 days ago by
Ram
39k • written 5 days ago by
Supernova
• 0
0
votes
0
replies
102
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course
RNA-seq
pathway
updated 5 days ago by
Ram
39k • written 5 days ago by
Fred
• 0
0
votes
1
reply
147
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 5 days ago by
Ram
39k • written 5 days ago by
chengc2016zzu
• 0
0
votes
0
replies
83
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase
Databases
enzymes
Restriction
5 days ago by
Mahmoud Reda
▴ 10
1
vote
2
replies
201
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
4 days ago by
Pegasus
▴ 90
0
votes
0
replies
120
views
Merging multiple PLINK files
plink
merging
6 days ago by
Nejla
• 0
0
votes
0
replies
117
views
References selected by ExomeDepth CNV
CNV
ExomeDepth
updated 6 days ago by
GenoMax
129k • written 6 days ago by
keiko.asakura
• 0
0
votes
2
replies
223
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
4 days ago by
J.F.Jiang
▴ 900
0
votes
2
replies
202
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping
Variant-calling
masking
updated 6 days ago by
Ram
39k • written 6 days ago by
Joel Wallenius
▴ 130
1
vote
3
replies
702
views
Regular Expression for conversion
Linux
grep
updated 5 days ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
0
votes
1
reply
165
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 5 days ago by
Ram
39k • written 6 days ago by
barrypraveen
▴ 110
0
votes
2
replies
173
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
6 days ago by
pg45863
• 0
0
votes
1
reply
139
views
ABySS Process Killed
ABySS
genome
assembly
updated 6 days ago by
GenoMax
129k • written 6 days ago by
asarcillo
• 0
0
votes
0
replies
97
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
6 days ago by
narges.bioinf
• 0
0
votes
3
replies
224
views
Query qbout single cell sequencing
fastq
ScRNA
updated 5 days ago by
Ram
39k • written 6 days ago by
abbas.waseem.gcu
▴ 20
0
votes
1
reply
181
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 5 days ago by
fracarb8
▴ 950 • written 7 days ago by
Sun
• 0
0
votes
1
reply
178
views
Why coordinate sort is required in sambamba depths?
sorting
coordinate
sambamba
linux
samtools
updated 7 days ago by
Pierre Lindenbaum
154k • written 7 days ago by
MobiusT
▴ 10
0
votes
4
replies
282
views
I need help with a methyl array data analysis
methyl_array
DMPs
DMRs
beta_value
r
7 days ago by
Ahmad
▴ 10
0
votes
2
replies
248
views
Error in download library file in expression console software
expression
microarray
console
5 days ago by
Mohammad
• 0
0
votes
6
replies
340
views
Demultiplexing bam file
demultiplexing
bam_file
Iontorrent
6 days ago by
hasani.iut6
▴ 60
1
vote
2
replies
264
views
DEgs RNAseq
RNAseq
7 days ago by
Juan
• 0
0
votes
0
replies
175
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
5 days ago by
Vincent Laufer
★ 2.9k
0
votes
1
reply
241
views
problem of Global Biobank Meta-analysis Initiative
GWAS
updated 7 days ago by
Fabio Marroni
★ 3.0k • written 8 days ago by
1362321710
• 0
1
vote
1
reply
229
views
DownsampleSam
picard
DownsampleSam
updated 8 days ago by
Pierre Lindenbaum
154k • written 8 days ago by
mathalfilip
• 0
0
votes
1
reply
237
views
Error while running Megahit
Megahit
updated 7 days ago by
Mensur Dlakic
★ 23k • written 8 days ago by
abhiramiabhirami9072
• 0
2
votes
5
replies
414
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
5 days ago by
DanielEB_fisk
• 0
1,000 results • Page
2 of 20
Recent Votes
How to make the profile line of `deepTools::plotHeatmap` more smooth?
Answer: How to make the profile line of `deepTools::plotHeatmap` more smooth?
Comment: Getting species names and taxa id from assembly accession number
Comment: STAR GenomeIndex output (which is the BAM file?)
Answer: [Meta] Use of AI
Answer: h5ad cellxgene to R
Comment: What is the benefit of knowing the source of contamination when we have RNAseq d
Recent Locations •
All
United States,
1 minute ago
Connecticut,
2 minutes ago
Canada/London/Western University,
2 minutes ago
China,
11 minutes ago
United States,
16 minutes ago
Moscow,
38 minutes ago
United States,
56 minutes ago
Recent Awards •
All
Popular Question
to
benformatics
3.6k
Popular Question
to
Dan
▴ 120
Supporter
to
rfran010
▴ 110
Popular Question
to
Siavash Salek Ardestani
▴ 20
Popular Question
to
Nai
▴ 50
Popular Question
to
Arindam Ghosh
▴ 500
Commentator
to
SmallChess
▴ 630
Recent Replies
Comment: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
by
Kevin Blighe
85k
Hello friend. Life moves on...
Comment: How to make the profile line of `deepTools::plotHeatmap` more smooth?
by
Dan
▴ 120
Do you mean I should check the intersections between the peaks in the `bed` file using `bedtools intersect` (https://bedtools.readthedocs.i…
Answer: How to make the profile line of `deepTools::plotHeatmap` more smooth?
by
Trivas
★ 1.2k
Your issue is with your bed file then, not necessarily with deep tools. I'd look into the bedtools suite to see if you can minimize overlap…
Comment: variant allelic fraction
by
Pierre Lindenbaum
154k
https://www.biostars.org/p/492331/
Comment: variant allelic fraction
by
malm
• 0
ok how can i calculate it from the vep file?
Comment: Filtering mitochondrial reads from ATAC-Seq aligned reads- what to do with reads
by
benformatics
3.6k
I think it would be fair (and conservative) to remove read pairs where one maps to the mitochondrial genome. It should be a relatively very…
Answer: Convert Bam file to Fastq
by
Michael
52k
I think your code is incorrect bash syntax. I think you want something like this: sort bam_headers.txt > bam_haeders-sorted.txt # c…
Comment: Combination of ROC CURVE
by
Maria17
▴ 20
For example, if three targets are combined and the mean value is plotted, the different combinations give different numbers, but there are …
Comment: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
by
Kermit
▴ 80
neither simple nor helpful, but perhaps the OP changed his question away from "why might diff models produce diff results" to the current "…
Comment: Convert Bam file to Fastq
by
Michael
52k
At first, I would trust samtools to do the right thing but of course it doesn't hurt to double check. But I think the crux is what is in fa…
Comment: Convert Bam file to Fastq
by
Pierre Lindenbaum
154k
paste fastq1_read_ids.txt fastq2_read_ids.txt is a tabular file with two column. Is it the same for bam_read_names.txt ?
Comment: variant allelic fraction
by
Pierre Lindenbaum
154k
this is not a field provided by VEP.
Answer: WGCNA Trait File Issues
by
Jennifer M
• 0
![enter image description here][1] [1]: /media/images/0cf4eaa7-9550-4bbb-b43e-208dc787
Comment: Pairwise Alignment
by
WouterDeCoster
47k
> for whole genome analysis What do you mean with that? You provide too little information for us to answer your question.
Comment: Getting species names and taxa id from assembly accession number
by
GenoMax
129k
There must be some temporary glitch. Following command works (via EntrezDirect): $ esearch -db assembly -query GCA_000001405.29 | esu…
Traffic: 1403 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