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148 results • Page
1 of 3
Sort: Votes
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Views
Votes
Replies
7
votes
7
replies
4.4k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 3 days ago by
Ram
39k • written 4.4 years ago by
stu111538
▴ 80
5
votes
4
replies
1.5k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection
DE-genes
multi-treatments
time-series
updated 3 days ago by
Ram
39k • written 6.9 years ago by
statfa
▴ 720
4
votes
4
replies
344
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 3 days ago by
Joe
21k • written 7 days ago by
antoine.fauchois92
▴ 20
4
votes
7
replies
2.2k
views
low bootstrap value?
phylogeny
genome
alignment
updated 2 days ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 1 day ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
4
votes
8
replies
1.6k
views
How to extract promoter sequences from a plant draft genome?
promoter
genome
updated 13 hours ago by
Ram
39k • written 3.7 years ago by
Kumar
▴ 100
4
votes
4
replies
249
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 1 day ago by
ATpoint
72k • written 1 day ago by
bioinfo
▴ 80
3
votes
7
replies
1.1k
views
Find 3'UTRs for species
Assembly
alignment
updated 14 hours ago by
Ram
39k • written 3.8 years ago by
Palgrave
▴ 110
3
votes
12
replies
2.1k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 1 day ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
3
votes
16
replies
9.9k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 3 days ago by
Ram
39k • written 4.2 years ago by
Star
▴ 60
2
votes
3
replies
1.2k
views
mutational signatures in different tumor samples
somatic mutation
mutational signature
updated 1 day ago by
Vincent Laufer
★ 2.9k • written 4.4 years ago by
lzy
▴ 20
2
votes
4
replies
224
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 2 days ago by
Ram
39k • written 2 days ago by
miguellarrazlopezdenovales
• 0
2
votes
0
replies
724
views
Why are there multiple bax/fastq files associated with my PacBio run?
genome
PacBio
WGS
sequencing
updated 3 days ago by
Ram
39k • written 4.1 years ago by
nickvpinkham
▴ 20
2
votes
1
reply
1.8k
views
How do I apply a patch to hg38?
reference
human
freeze
hg38
patch
updated 1 day ago by
Jeremy Leipzig
21k • written 5.6 years ago by
imperialcommando117
• 0
2
votes
3
replies
690
views
Including bioinformatics into an agriculture/horticulture dissertation project
agrobioinformatics
plant-gene-analysis
updated 3 days ago by
Ram
39k • written 4.1 years ago by
cipri91rusu
• 0
2
votes
6
replies
1.0k
views
Time series RNA seq design query
RNA-seq
time-series
deseq2
updated 3 days ago by
Ram
39k • written 18 months ago by
kra277
• 0
2
votes
2
replies
168
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 1 day ago by
Dr William Klubinski
▴ 80 • written 2 days ago by
linnet.roque6
▴ 10
2
votes
3
replies
143
views
Low mapping percentage
mapping
STAR
RNAseq
23 minutes ago by
Sib
▴ 40
2
votes
5
replies
405
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
3 days ago by
DanielEB_fisk
• 0
1
vote
3
replies
165
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 2 days ago by
Pierre Lindenbaum
154k • written 3 days ago by
herh
• 0
1
vote
0
replies
114
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
1 day ago by
abba647
▴ 10
1
vote
1
reply
136
views
Combination of ROC CURVE
roccurve
R
AUC
updated 1 day ago by
seidel
11k • written 1 day ago by
Maria17
▴ 20
1
vote
1
reply
2.6k
views
Comparing time series expression data
time-series
gene-expression
updated 3 days ago by
Ram
39k • written 5.8 years ago by
The
▴ 180
1
vote
1
reply
227
views
DownsampleSam
picard
DownsampleSam
updated 6 days ago by
Pierre Lindenbaum
154k • written 6 days ago by
mathalfilip
• 0
1
vote
4
replies
1.5k
views
Time series event recurrence comparison
recurrence
time-series
updated 3 days ago by
Ram
39k • written 6.7 years ago by
Nicolas Rosewick
10k
1
vote
5
replies
3.6k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis
Time-series
pairwise
updated 3 days ago by
Ram
39k • written 6.8 years ago by
Biogeek
▴ 470
1
vote
0
replies
226
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 3 days ago by
Ram
39k • written 4 days ago by
Supernova
• 0
1
vote
0
replies
102
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
2 days ago by
fr
▴ 200
1
vote
0
replies
1.3k
views
NCBI Taxon ID to IMG Genome IDs
taxon
html
updated 1 day ago by
Ram
39k • written 3.9 years ago by
Mohak
▴ 20
1
vote
3
replies
209
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 2 days ago by
GenoMax
129k • written 2 days ago by
mls
• 0
1
vote
0
replies
444
views
Using STAR SJ.out.tab file to identify novel ncRNAs
time-course
RNA-seq
ncRNA
STAR
updated 3 days ago by
Ram
39k • written 17 months ago by
jennifer.conrad84
▴ 10
1
vote
2
replies
160
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 18 hours ago by
thadjudkins2
• 0 • written 1 day ago by
herh
• 0
1
vote
1
reply
1.6k
views
Bioinformatics tools for Plasmid detection
short-read
plasmid
updated 1 day ago by
Ram
39k • written 3.9 years ago by
El Niño
▴ 10
1
vote
1
reply
105
views
Create customized gene annotation file
reference-genome
cellranger
updated 2 days ago by
Ram
39k • written 3 days ago by
rhonddaskl
• 0
1
vote
2
replies
197
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
2 days ago by
Pegasus
▴ 90
1
vote
7
replies
5.6k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 4 days ago by
dare_devil
★ 3.1k • written 5.3 years ago by
win
▴ 940
1
vote
1
reply
121
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 2 days ago by
GenoMax
129k • written 2 days ago by
hashim.rana11
▴ 20
1
vote
1
reply
3.1k
views
Problem with PGDSpider v 2.1.0.2
alignment
updated 2 days ago by
sackettl
▴ 20 • written 7.0 years ago by
maria.segovia.ramirez
▴ 10
1
vote
0
replies
74
views
Bayesian network for biological data using bnlearn
bnlearn
RNA-seq
bayesian-network
updated 17 hours ago by
Ram
39k • written 22 hours ago by
priyankamehta.1811
▴ 10
1
vote
3
replies
180
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 1 day ago by
GenoMax
129k • written 2 days ago by
NikhilP
▴ 20
1
vote
4
replies
354
views
Pre-processing for Agilent microarray data?
affymetrix
microarray
gene
agilent
rna
updated 5 days ago by
solarchan7
• 0 • written 10 days ago by
survive
• 0
1
vote
2
replies
257
views
DEgs RNAseq
RNAseq
5 days ago by
Juan
• 0
1
vote
0
replies
89
views
Resequencing data of pangenome
NGS
PanGenome
Resequence
updated 3 days ago by
Ram
39k • written 3 days ago by
bioinfo223
▴ 10
1
vote
0
replies
82
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
1 day ago by
Jonathan Lefebre
▴ 50
1
vote
1
reply
241
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 22 hours ago by
GenoMax
129k • written 23 hours ago by
Mohd
▴ 20
1
vote
3
replies
700
views
Regular Expression for conversion
Linux
grep
updated 3 days ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
1
vote
5
replies
2.3k
views
Calculating distance matrix of RNA-seq data
Dynamic-Time-Warping
R
time-series
updated 3 days ago by
Ram
39k • written 5.2 years ago by
fi1d18
★ 4.2k
1
vote
2
replies
160
views
sorting BAM file
BAM
updated 3 days ago by
ATpoint
72k • written 3 days ago by
Mohammad Amin
• 0
0
votes
0
replies
796
views
Simulating Time Course RNA-Seq Data With Polyester
Time-Course
RNA-Seq
updated 3 days ago by
Ram
39k • written 4.0 years ago by
eashby47
▴ 10
0
votes
2
replies
198
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping
Variant-calling
masking
updated 4 days ago by
Ram
39k • written 4 days ago by
Joel Wallenius
▴ 130
148 results • Page
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Comment: Low mapping percentage
Comment: Low mapping percentage
A: genomicranges outside sequence bounds
A: how can i download human ribosomal reference ?
Bayesian network for biological data using bnlearn
Comment: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
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Comment: Low mapping percentage
by
Sib
▴ 40
Thank you for the reply. If there is not much I can do about the contamination at this stage, what is the benefit of knowing the source of…
Answer: integrate single cell RNA sequencing data
by
Hamid Ghaedi
2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP
by
Vincent Laufer
★ 2.9k
@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
Comment: Help with running ATAC using Encode pipeline
by
Chris
▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs
by
rycro_c
• 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage
by
Dave Carlson
★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order?
by
Pierre Lindenbaum
154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage
by
GenoMax
129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences
by
GenoMax
129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files
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Joe
21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences
by
sodiumnitrate
▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
GenoMax
129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order?
by
GenoMax
129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column
by
atemedorri137798
• 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order?
by
Ram
39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
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