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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
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
7
votes
12
replies
1.1k
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
▴ 180
5
votes
12
replies
863
views
Data from an experiment
single-cell
updated 7 months ago by
GenoMax
134k • written 7 months ago by
Chris
▴ 180
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
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
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
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
942
views
Help with error in cellranger
Cellranger
updated 4 months ago by
GenoMax
134k • written 4 months ago by
Chris
▴ 180
2
votes
12
replies
1.8k
views
The best way to get gene lengths for 15K+ genes?
r
EDAseq
RNA-seq
11 months ago by
JACKY
▴ 100
1
vote
12
replies
1.3k
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
672
views
scrna seq analysis - doublets
scrna
seq
code
r
updated 11 weeks ago by
Nitin Narwade
★ 1.4k • written 11 weeks ago by
bioinformatics
▴ 20
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
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
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 8.2 years ago by
mafireyi
▴ 80
1
vote
12
replies
3.9k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq
alignment
sequencing
updated 8 months ago by
ATpoint
76k • written 6.0 years ago by
SMILE
▴ 170
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
12 weeks ago by
Saurabh
• 0
1
vote
12
replies
3.5k
views
dN/dS analysis of genomes
genome
sequence
alignment
11 months ago by
Mehmet
▴ 820
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
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
1.9k
views
i want to convert .ht2 files into FASTA file
GATK
HISAT2
FASTA
updated 3 months ago by
Ram
40k • written 4.3 years ago by
saumya.sharma1509
• 0
5
votes
11
replies
544
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 6 weeks ago by
Ram
40k • written 6 weeks ago by
Chris
▴ 180
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
4
votes
11
replies
2.9k
views
Please add an explicit type tag :NAME
software-error
next-gen
genome
updated 7 months ago by
Ram
40k • written 5.4 years ago by
mahdikhadem95
▴ 30
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
0
votes
11
replies
662
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
1 day ago by
evmae
• 0
4
votes
11
replies
897
views
PCA WITH PLINK
PLINK
updated 5 weeks ago by
Kevin Blighe
86k • written 5 weeks ago by
adriana michelle
• 0
6
votes
11
replies
1.2k
views
Calculate RPKM
RPKM
6 months ago by
Chris
▴ 180
5
votes
11
replies
703
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 6 weeks ago by
cmdcolin
★ 3.2k • written 6 weeks ago by
pablo
▴ 280
2
votes
11
replies
1.4k
views
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided)
repeatmasker
updated 21 days ago by
rfran010
▴ 790 • written 5 weeks ago by
epianalysis
• 0
0
votes
11
replies
1.4k
views
count file having zero
RNA-Seq
next-gen
alignment
updated 3 months ago by
Ram
40k • written 4.6 years ago by
BioBaby
▴ 20
7
votes
10
replies
1.4k
views
col as names [solved]
R
updated 6 months ago by
Ram
40k • written 4.5 years ago by
demoraesdiogo2017
▴ 90
1
vote
10
replies
2.7k
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 3 months ago by
Ram
40k • written 4.5 years ago by
Kumar
▴ 120
4
votes
10
replies
706
views
Check Strandedness
Check_Strandedness
how_are_we_stranded_here
leafcutter
bash
29 days ago by
Y
• 0
0
votes
10
replies
340
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
1 day ago by
Y
• 0
3
votes
10
replies
348
views
STAR index not working
STAR
RNA-Seq
8 hours ago by
camillab.
▴ 130
2
votes
10
replies
1.3k
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
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
7.3k
views
Error: reads file does not look like a fastq file
fastq
bowtie2
ChIP-Seq
updated 6 months ago by
Ram
40k • written 7.0 years ago by
addilynn.beach
▴ 40
0
votes
10
replies
2.3k
views
WGCNA, module trait relationship
R
updated 11 months ago by
priya.bmg
▴ 60 • written 3.1 years ago by
sadeghi.reyhane
• 0
4
votes
10
replies
602
views
Extract unmapped reads OR reads covering chromosome 6 from a bam file?
fastq
bam
samtools
picard
7 months ago by
dps2501
▴ 20
0
votes
10
replies
1.7k
views
DeSeq2 "some values in assay are negative"
RNAseq
10 months ago by
Morris_Chair
▴ 340
0
votes
10
replies
662
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
21 days ago by
langziv
▴ 50
1
vote
10
replies
1.9k
views
Weird results for scRNA-seq
scRNA-seq
GEO
updated 8 months ago by
Giuseppe
▴ 70 • written 9 months ago by
tujuchuanli
▴ 100
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
5
votes
10
replies
589
views
Error when viewing a bam file
samtools
updated 3 months ago by
Ram
40k • written 4 months ago by
Chris
▴ 180
8
votes
10
replies
1.4k
views
PyWGCNA
WGCNA
3 months ago by
yoshifumimiya
▴ 40
1
vote
10
replies
5.5k
views
which field has more scope Bioinformatics or Biomedical engineering at MS level???
biomedical
updated 5 months ago by
Ram
40k • written 7.1 years ago by
purpledora100
• 0
1
vote
10
replies
818
views
Coverage histogram query
Alignment
27 days ago by
prasundutta87
▴ 660
1,000 results • Page
2 of 20
Recent Votes
Answer: Assistance with Fungal Genome Annotation Using Maker and BLAST
Salmon alignment based quantification
Comment: Salmon index not progressing
Answer: Adding a control sample to bulk RNA-seq
Comment: Adding a control sample to bulk RNA-seq
Comment: kallisto normalized TPM values without bootstraps
Comment: Identify Alternative Splicing Event using exon and junction count table
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Comment: Find potential important genes from bulk-RNA seq experiment
by
Michael
53k
You can use e.g. the WGCNA package for network analysis. In your case multiple samples this might mean multiple patients or a time series o…
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
edoardoscali.93
• 0
Thank you so much for your responses. @genomax , I've downloaded both of the databases you recommended. I attempted to combine them into …
Answer: Simulate short-read RNA-seq data from long-read RNA-seq data
by
Mensur Dlakic
★ 24k
I think you could try doing this, but it wouldn't be appropriate. You'd be bringing long-read errors, which I believe are higher than short…
Comment: Salmon index not progressing
by
camillab.
▴ 130
I opened tow terminals and one was the code to build a decoy-aware transcriptome and the other was building indexes (no decoy)
Comment: Adding a control sample to bulk RNA-seq
by
Chris
▴ 180
Thank you for the explanation! So just want to confirm one control with replicate is totally useless even can't use as a reference?
Answer: DESeq2 analysis using two featureCounts generated from different studies
by
swbarnes2
13k
Comparing samples between labs is a bad idea. Better to generate gene lists from one study from one lab, and gene lists from another study…
Comment: Adding a control sample to bulk RNA-seq
by
swbarnes2
13k
If a sample wasn't prepared along side your treated samples, it is a different batch. If you had treated and controls in each of two diffe…
Comment: kallisto normalized TPM values without bootstraps
by
ATpoint
76k
You don't need sleuth. Typically these deconvolutions, or most downstream analysis, is done on the gene- rather than the transcript-level w…
Comment: Salmon index not progressing
by
ATpoint
76k
If the top $CPU column shows some values in the hundreds then it is doing something (actually when it's > 0%). So based on the screenshot i…
Comment: Salmon index not progressing
by
camillab.
▴ 130
Thank you. Waiting it's not gonna hurt me, when should I stop hoping and give up is the question? do you know is there a way if I can see i…
Comment: Filtering VCF to divide with equal sizes
by
Ram
40k
A more efficient way would be to make a 2 column CSV file, one column with the count value and the other with the chr:start-end range, then…
Answer: Filtering VCF to divide with equal sizes
by
avelarbio46
▴ 30
I divided my contigs using R, but it was more complex than the program Pierre Lindenbaum made (https://jvarkit.readthedocs.io/en/latest/Vcf…
Comment: Salmon index not progressing
by
ATpoint
76k
Just wait until it is finished. It's seems to be running. I just checked my logs and on our HPC with four cores such as process for a decoy…
Comment: Salmon index not progressing
by
GenoMax
134k
> 2 hrs trying to generate decoy-aware transcriptome for human. is this time normal? It is probably normal considering resources you have…
Comment: Chromosome bias on RNA-Seq differential gene expression analysis
by
grant.hovhannisyan
★ 2.5k
you expect to have aneuploidy only in the knockout?
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