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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
1
vote
12
replies
3.5k
views
why different outputs with applying various extracting fasta sequences tool, which one correct!?
alignment
sequencing
RNA-Seq
updated 11 months ago by
Ram
40k • written 8.1 years ago by
seta
★ 1.8k
1
vote
12
replies
4.0k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq
alignment
sequencing
updated 8 months ago by
ATpoint
77k • written 6.0 years ago by
SMILE
▴ 170
1
vote
12
replies
3.5k
views
dN/dS analysis of genomes
genome
sequence
alignment
11 months ago by
Mehmet
▴ 820
7
votes
12
replies
1.2k
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA
integrated
ATAC-seq
updated 4 months ago by
Sasha
▴ 720 • written 4 months ago by
Chris
▴ 200
0
votes
12
replies
1.8k
views
bedtools intersect issue
bed
bedtools
updated 6 months ago by
Ram
40k • written 5.1 years ago by
elisheva
▴ 120
2
votes
12
replies
2.1k
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 6 months ago by
Ram
40k • written 6 months ago by
Human
• 0
0
votes
12
replies
2.8k
views
Allpaths- Keep getting ConvertToFastbQualb.pl failed for group 'paired_ends' when I run PrepareAllPaths
next-gen
Assembly
updated 9 months ago by
Ram
40k • written 8.3 years ago by
mafireyi
▴ 80
2
votes
12
replies
1.9k
views
The best way to get gene lengths for 15K+ genes?
r
EDAseq
RNA-seq
12 months ago by
JACKY
▴ 100
8
votes
12
replies
3.1k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 6 months ago by
Ram
40k • written 2.1 years ago by
daver.v
▴ 30
6
votes
12
replies
1.4k
views
VCF files 101 - for people from non Bioinformatics Background
vcf
sequencing
genome
variant-calling
updated 6 months ago by
Ram
40k • written 3.1 years ago by
akshaykum684
▴ 20
2
votes
12
replies
4.3k
views
Adding barcodes to forward and reverse reads after sequencing
obitools
barcoding
next-gen-sequencing
updated 7 months ago by
Ram
40k • written 8.4 years ago by
cmogren
▴ 20
5
votes
12
replies
885
views
Data from an experiment
single-cell
updated 7 months ago by
GenoMax
134k • written 7 months ago by
Chris
▴ 200
6
votes
12
replies
969
views
Help with error in cellranger
Cellranger
updated 4 months ago by
GenoMax
134k • written 4 months ago by
Chris
▴ 200
1
vote
12
replies
1.4k
views
Volcano plot interpretation
EnhancedVolcano
volcano-plot
updated 7 months ago by
Ram
40k • written 2.2 years ago by
fahim
▴ 20
0
votes
12
replies
705
views
scrna seq analysis - doublets
scrna
seq
code
r
updated 12 weeks ago by
Nitin Narwade
★ 1.4k • written 12 weeks ago by
bioinformatics
▴ 20
4
votes
12
replies
1.3k
views
Bulk RNA seq: all p adjusted are the same
p-adj
RNA-seq
differential-gene-expression
updated 9 months ago by
Ram
40k • written 16 months ago by
nils.simon.biology
▴ 10
0
votes
12
replies
3.0k
views
comparative analysis of two strains of bacteria's genomes
genome
gene
updated 4 months ago by
Ram
40k • written 5.9 years ago by
fonteneaudam
▴ 20
6
votes
12
replies
1.3k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r
biomarker
updated 6 months ago by
Ram
40k • written 4.7 years ago by
english.server
▴ 290
0
votes
12
replies
1.3k
views
Splitting CRAM files
CRAM-files
sequence-alignment
9 months ago by
langziv
▴ 50
1
vote
12
replies
1.1k
views
gatk Funcotator
vcf
Funcotator
gatk
3 months ago by
Saurabh
• 0
3
votes
12
replies
2.5k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 3 months ago by
Pegasus
▴ 90 • written 4.0 years ago by
mnazir
▴ 10
5
votes
11
replies
563
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 7 weeks ago by
Ram
40k • written 7 weeks ago by
Chris
▴ 200
5
votes
11
replies
3.3k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 6 months ago by
Ram
40k • written 5.4 years ago by
HG
▴ 30
6
votes
11
replies
1.2k
views
Calculate RPKM
RPKM
6 months ago by
Chris
▴ 200
0
votes
11
replies
1.4k
views
count file having zero
RNA-Seq
next-gen
alignment
updated 3 months ago by
Ram
40k • written 4.7 years ago by
BioBaby
▴ 20
4
votes
11
replies
2.9k
views
Please add an explicit type tag :NAME
software-error
next-gen
genome
updated 8 months ago by
Ram
40k • written 5.4 years ago by
mahdikhadem95
▴ 30
5
votes
11
replies
730
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 7 weeks ago by
cmdcolin
★ 3.2k • written 7 weeks ago by
pablo
▴ 280
0
votes
11
replies
1.9k
views
i want to convert .ht2 files into FASTA file
GATK
HISAT2
FASTA
updated 3 months ago by
Ram
40k • written 4.4 years ago by
saumya.sharma1509
• 0
0
votes
11
replies
742
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
8 days ago by
evmae
• 0
1
vote
11
replies
3.3k
views
bedtools fisher interpretation of "in -a" "not in -b"
fisher
bedtools
intersection
updated 7 months ago by
Ram
40k • written 5.6 years ago by
jomo018
▴ 720
1
vote
11
replies
775
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 4 days ago by
GenoMax
134k • written 4 weeks ago by
langziv
▴ 50
4
votes
11
replies
932
views
PCA WITH PLINK
PLINK
updated 6 weeks ago by
Kevin Blighe
86k • written 6 weeks ago by
adriana michelle
• 0
1
vote
11
replies
3.4k
views
merge samples in phyloseq returns NAs
R
phyloseq
biom
updated 10 months ago by
joe.e.weaver
• 0 • written 3.2 years ago by
annaA
▴ 10
0
votes
11
replies
1.1k
views
Problem with Trimmomatic Multiple Paired-End sequencing.
Trimmomatic
updated 8 months ago by
GenoMax
134k • written 8 months ago by
john
• 0
1
vote
10
replies
779
views
Do monoclonal antibodies have a blocking effect?
block
antibody
offtopic
updated 5 weeks ago by
Jeremy
▴ 840 • written 5 weeks ago by
jinyu
▴ 10
4
votes
10
replies
749
views
Check Strandedness
Check_Strandedness
how_are_we_stranded_here
leafcutter
bash
5 weeks ago by
Y
• 0
7
votes
10
replies
1.5k
views
Ubuntu 20.04 Crash
Ubuntu
updated 7 months ago by
Ram
40k • written 20 months ago by
bala
• 0
4
votes
10
replies
3.8k
views
TCGA normalized count data of 1000 samples for DGE
RNA-Seq
TCGA
updated 8 months ago by
Ram
40k • written 8.4 years ago by
David_emir
▴ 470
7
votes
10
replies
1.4k
views
col as names [solved]
R
updated 6 months ago by
Ram
40k • written 4.6 years ago by
demoraesdiogo2017
▴ 90
1
vote
10
replies
2.8k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 4 months ago by
Ram
40k • written 4.5 years ago by
Kumar
▴ 120
2
votes
10
replies
1.4k
views
multiple FASTA sequnces in to one full sequnce according to their chromosome number
NGS
FASTA
bam
updated 6 months ago by
Ram
40k • written 4.6 years ago by
Anu
• 0
4
votes
10
replies
618
views
Extract unmapped reads OR reads covering chromosome 6 from a bam file?
fastq
bam
samtools
picard
7 months ago by
dps2501
▴ 20
5
votes
10
replies
602
views
Error when viewing a bam file
samtools
updated 3 months ago by
Ram
40k • written 4 months ago by
Chris
▴ 200
2
votes
10
replies
4.0k
views
Error encountered while running stattest from ballgown package
bioconductor
RNA-Seq
ballgown
stattest
updated 5 months ago by
Ram
40k • written 6.4 years ago by
lakhujanivijay
5.8k
2
votes
10
replies
6.7k
views
fq.gz file use
BioEdit
R
updated 6 months ago by
Ram
40k • written 4.6 years ago by
choi.yisoo.hi
• 0
0
votes
10
replies
1.7k
views
DeSeq2 "some values in assay are negative"
RNAseq
10 months ago by
Morris_Chair
▴ 340
1
vote
10
replies
2.0k
views
Weird results for scRNA-seq
scRNA-seq
GEO
updated 9 months ago by
Giuseppe
▴ 70 • written 9 months ago by
tujuchuanli
▴ 100
3
votes
10
replies
512
views
STAR index not working
STAR
RNA-Seq
6 days ago by
camillab.
▴ 140
2
votes
10
replies
1.4k
views
R-studio freezes error
RStudio
offtopic
updated 11 months ago by
Ram
40k • written 11 months ago by
Amr
▴ 140
8
votes
10
replies
1.5k
views
PyWGCNA
WGCNA
3 months ago by
yoshifumimiya
▴ 40
1,000 results • Page
2 of 20
Recent Votes
C: How Do I Convert Fa Files To Bed Format?
Clustering in single cell
Answer: Network analysis with cytoscape
Answer: Network analysis with cytoscape
Network analysis with cytoscape
Comment: How to convert data in r?
Comment: Frustrated with DEA results
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Recent Replies
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
ella
• 0
I think I even used `reformat.sh` earlier today, but don´t remember with what arguments. I now tried what you suggested, but got an error: …
Comment: Clustering in single cell
by
Jean-Karim Heriche
26k
Are you doing the clustering in UMAP space? If so, avoid distance-based clustering because distances are only meaningful locally, i.e dista…
Comment: Github access with token headache
by
Ram
40k
Yes please.
Comment: How to convert data in r?
by
Ram
40k
> tidyr does not make anything tidy at all I don't get your point. The code does not use tidyr (`%>%` is from `magrittr`) and there is no …
Comment: Unmapped Reads in Kallisto
by
GenoMax
134k
https://www.biostars.org/u/30020/ you can add a solution to this thread. It looks like this poster has a similar issue described in origina…
Comment: Unmapped Reads in Kallisto
by
dsull
★ 4.7k
Create a new thread if you need help with this.
Comment: Network analysis with cytoscape
by
Chris
▴ 200
Thanks xanderpico! That is great resources. There are many bioinformatics tools now which is hard to choose an appropriate one. I found thi…
Comment: Frustrated with DEA results
by
dsull
★ 4.7k
Great suggestion on visualizing the data as well as doing DE between variables that you know should result in different gene expression pro…
Answer: Network analysis with cytoscape
by
xanderpico
▴ 500
Hi Chris. There are dozens of different directions you could go using Cytoscape. There is not just one analysis path. You mention "tran…
Comment: How to convert data in r?
by
Jeremy
▴ 840
Great answer bk11. star, you'll need the dplyr package to run this code. Just make the following the first line of code: library(dpl…
Comment: Troubles launch IGV on Linux(Debian)
by
PoscaXVIII
• 0
Hi barslmn, Thank you so much for your help it works perfectly. No more frozen black screen. I just changed from wayland to Xorg (On the pa…
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
by
LChart
3.4k
> I tried a general "overall" group comparison of the "general" conditions, trying to model the "donor" effect and including it into the de…
Comment: How to convert data in r?
by
Kevin Blighe
86k
Funny how *tidyr* does not make anything tidy at all. Why not just use (actually less characters): data <- data.frame(c( "A \t 22…
Comment: Frustrated with DEA results
by
Jeremy Leipzig
21k
If the FDR is killing your results, it's ok to filter out genes that are not informative https://www.bioconductor.org/help/course-materials…
Comment: Github access with token headache
by
Begonia_pavonina
▴ 110
I will post it in StackOverflow, should I delete this thread?
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