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707 results • Page
2 of 15
Sort: replies
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Views
Votes
Replies
0
votes
9
replies
408
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
7 days ago by
njornet
▴ 20
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 24 days ago by
Ram
44k • written 9 months ago by
Gio
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
24 days ago by
anna
▴ 20
1
vote
8
replies
590
views
Downsampling fastq file
downsample
fastq
23 days ago by
marco.barr
▴ 130
1
vote
8
replies
985
views
Adding CB tag to bam file
samtools
bam
updated 28 days ago by
Pierre Lindenbaum
162k • written 4 weeks ago by
Maria
• 0
3
votes
8
replies
750
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 16 days ago by
Chris Dean
▴ 410 • written 21 days ago by
sovrappensiero
▴ 100
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 20 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
8
replies
547
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 3 days ago by
Pierre Lindenbaum
162k • written 12 days ago by
ajbarrett98
• 0
0
votes
8
replies
555
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 22 days ago by
LauferVA
4.2k • written 24 days ago by
jinyu
▴ 10
1
vote
8
replies
837
views
Random Access remote BAM files
htslib
BAM
updated 19 hours ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 10
0
votes
8
replies
514
views
Different output for read length
samtools
BAM
13 days ago by
marco.barr
▴ 130
1
vote
8
replies
496
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 5 days ago by
Alex Reynolds
35k • written 9 days ago by
ntsopoul
▴ 60
2
votes
8
replies
417
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 11 days ago by
Pierre Lindenbaum
162k • written 11 days ago by
Matteo Ungaro
▴ 100
3
votes
8
replies
650
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
16 days ago by
Qroid
▴ 40
8
votes
8
replies
799
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 28 days ago by
swbarnes2
14k • written 29 days ago by
Aaliya
▴ 10
0
votes
7
replies
684
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 20 days ago by
LChart
3.9k • written 24 days ago by
kl
▴ 10
4
votes
7
replies
452
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
9 days ago by
Chen
• 0
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 5 days ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
1
vote
7
replies
631
views
gvcf joint calling
WES
GATK
VCF
gVCF
25 days ago by
zihanss
• 0
3
votes
7
replies
440
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
24 days ago by
Sergio A.S.
• 0
4
votes
7
replies
650
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
24 days ago by
e.r.zakiev
▴ 210
0
votes
7
replies
483
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 10 days ago by
Mohamed Abderrahmane
▴ 20 • written 24 days ago by
matteo.levorato
• 0
2
votes
7
replies
599
views
KEGG analysis in R
KEGG
clusterProfiler
Zea-mays
updated 1 day ago by
letizia.ottaviani
• 0 • written 6 weeks ago by
sansan_96
▴ 90
4
votes
7
replies
636
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 28 days ago by
dsull
★ 6.1k • written 29 days ago by
VITALA
• 0
1
vote
7
replies
531
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
20 days ago by
eebloom
▴ 80
1
vote
7
replies
631
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 24 days ago by
bk11
★ 2.5k • written 28 days ago by
starswillfade
▴ 10
5
votes
7
replies
552
views
RNA seq analysis
DESeq
RNA-seq
8 days ago by
Jacek
▴ 20
3
votes
7
replies
3.9k
views
Difference in Bismark output methylation call files and coverage files
RRBS
Bismark
DNA-methylation
updated 2 hours ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
1
vote
7
replies
592
views
Question regarding WGCNA
WGCNA
Network-construction
14 days ago by
deepak
• 0
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 24 days ago by
Gordon Smyth
★ 7.2k • written 8 months ago by
Calum
▴ 10
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 28 days ago by
rohitsatyam102
▴ 870 • written 6.2 years ago by
smallfish
▴ 10
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 12 days ago by
Ruqaiya
• 0 • written 5.8 years ago by
xiaozhongzhiping
▴ 20
6
votes
7
replies
426
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
10 days ago by
sansan_96
▴ 90
6
votes
6
replies
1.9k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 18 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
5
votes
6
replies
643
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 23 days ago by
me
▴ 760 • written 24 days ago by
Mariana
▴ 40
1
vote
6
replies
770
views
anRichment is missing
WGCNA
anRichment
updated 17 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
0
votes
6
replies
512
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 19 days ago by
swbarnes2
14k • written 20 days ago by
Erina
• 0
0
votes
6
replies
476
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
29 days ago by
Sd
• 0
2
votes
6
replies
3.8k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 27 days ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 7 days ago by
Ram
44k • written 3.9 years ago by
millere
• 0
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 27 days ago by
Antonio R. Franco
★ 5.1k • written 6.1 years ago by
williamsbrian5064
▴ 520
1
vote
6
replies
260
views
samtools write-index
samtools
updated 6 hours ago by
aw7
▴ 310 • written 1 day ago by
LucisTheFather
• 0
3
votes
6
replies
325
views
Problem in getting geo file through GEOQUERY
geoquery
Geo
updated 22 hours ago by
Ram
44k • written 1 day ago by
anasjamshed
▴ 120
1
vote
6
replies
438
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 20 days ago by
GenoMax
142k • written 5 weeks ago by
eebloom
▴ 80
0
votes
6
replies
2.2k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 14 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
3
votes
6
replies
543
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 10 days ago by
Pine
▴ 20 • written 18 days ago by
snajafy
• 0
3
votes
6
replies
2.1k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 26 days ago by
Ram
44k • written 2.4 years ago by
SYOSY
▴ 10
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 24 days ago by
dimpleadiwal050896
• 0 • written 5.0 years ago by
ggman
▴ 90
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 15 days ago by
chenl
▴ 10 • written 2.6 years ago by
Martyna
• 0
4
votes
6
replies
832
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 26 days ago by
dsull
★ 6.1k • written 4 weeks ago by
qudrat.nii
▴ 10
707 results • Page
2 of 15
Recent Votes
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Downloading NCBI Blast nt database
Comment: log2 fold change in RNA-seq analysis
Comment: log2 fold change in RNA-seq analysis
Answer: Ideal PC configurations and operating system for bioinformatics laboratory
correct way of analyzing cell proportions in singlecell data
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Comment: What do the transcript variant # mean in RefSeq?
by
GenoMax
142k
> What do these correspond to? It does not seem to be the longest transcript. Is it the canonical transcript? Those are just different tra…
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
jared.andrews07
★ 17k
MGI has a [Gene Expression Database](https://www.informatics.jax.org/expression.shtml) that'll largely get you what you want.
Comment: Difference in Bismark output methylation call files and coverage files
by
Papyrus
★ 2.9k
Your files end in `CpG_report` so they are the "genome-wide cytosine report output". If you look at the [Bismark documentation][1] you will…
Answer: Error when looping over multiple columns in a data frame in R
by
Mohamed Samir
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Dear Jeremy, Thanks. What I could not understand why you wrote it like : cutpoint_results[[col_name]] ? Is it because it is a list result…
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44k
Do not use all caps - it's bad etiquette. I've fixed things for you this time.
Comment: minfi::getQC - badsamplecutoff 10.5
by
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★ 2.9k
I've recently also analyzed EPICv2 and have noticed that the log2 median intensities (and particularly the "uMed" channel), for an otherwis…
Comment: log2 fold change in RNA-seq analysis
by
May Ling
• 0
Thank you so much for the confirmation Sir! Appreciate that. I think the paragraph was trying to say that: a fold change greater than **…
Comment: Difference in Bismark output methylation call files and coverage files
by
skdv2522
• 0
Chr1 192 + 0 0 CG CGA Chr1 193 - 0 0 CG CGA Chr1 197 + 0 0 CG CGT Chr1 198 - 0 0 CG CGG Chr1 218 + 0 0 CG CGA Chr1 …
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cross-posted: https://stackoverflow.com/questions/78522566/ > Do not post on multiple forums - that is just bad etiquette. What's worse, y…
Comment: log2 fold change in RNA-seq analysis
by
dsull
★ 6.1k
Your understanding is correct. That attached highlighted sentence is wrong.
Comment: minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of s
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Hello, I just started working on analyzing methylation EPIC array data using minfi. Data is generated on EPICv2 array and I'm using up…
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Please do not add answers unless you're actually answering the top level question. Open your own question if the forum has not addressed it…
Comment: log2 fold change in RNA-seq analysis
by
May Ling
• 0
Thank you for your prompt reply Sir! I think I finally understand the concept. Please correct me if I'm wrong: Let's say we are comparing …
Comment: log2 fold change in RNA-seq analysis
by
Hatchet
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He means that the result of DEA will contain DEGs of A vs B. He gets LFC numbers in one column and positive LFC numbers will mean positive …
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Akash D
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I made this. Z scored on log2FC? will anyone support me on this? 3 groups A,B,C
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