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1,000 results • Page 5 of 20
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8
votes
3
replies
1.2k
views
Package installation error using Bioconda
antismash Bioconda
17 months ago by A_heath ▴ 160
8
votes
9
replies
3.0k
views
6 follow
Big difference in estimated duplicate reads between forward and reverse of paired-end RNA-seq
RNA-Seq duplication fastqc
updated 23 months ago by ▴ 860 • written 4.5 years ago by ★ 2.1k
8
votes
30
replies
5.2k
views
Per Base Sequence Content
sequencing fastqc genome sequence
updated 4.1 years ago by ▴ 560 • written 4.1 years ago by ▴ 20
8
votes
6
replies
2.6k
views
for low coverage RNAseq how many reads assigned is the bare minimum for differential gene expression analysis
RNA-Seq
5.2 years ago by senowinski ▴ 30
8
votes
5
replies
1.0k
views
Why could we infer a physical time scale (e.g. a billion year) from a phylogenetic analysis?
phylogeny phylogenetic tree
4.5 years ago by johnnytam100 ▴ 110
8
votes
5
replies
2.0k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 7 months ago by 43k • written 2.6 years ago by ▴ 160
8
votes
4
replies
2.3k
views
Implementing a naive javascript-based de Bruijn graph
debruijn graph javascript algorithm
8.0 years ago by Pierre Lindenbaum 161k
8
votes
8
replies
1.8k
views
6 follow
DESeq2 adjusted p-values of 0 when p-value > 0.05
RNA-seq DEseq2
updated 3.0 years ago by ▴ 390 • written 3.0 years ago by • 0
8
votes
6
replies
2.3k
views
Using Bandage to finish ambiguous long-read assembly?
Assembly Bandage long reads Unicycler
updated 5.3 years ago by 20 • written 5.4 years ago by ★ 2.0k
8
votes
20
replies
3.0k
views
Why does cufflinks split this transcript?
RNA-Seq cufflinks assembly
6.3 years ago by corend ▴ 70
8
votes
12
replies
4.3k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 14 months ago by 43k • written 2.8 years ago by ▴ 30
8
votes
6
replies
1.2k
views
I have 2 identical jupyter notebooks and I get BiomartException when I run one but not the other.
biomart python
updated 4.3 years ago by 20 • written 4.3 years ago by ▴ 50
8
votes
13
replies
2.5k
views
Issue about install Cutadapt in ubuntu1404
cutadapt
7.1 years ago by Joe ▴ 30
8
votes
7
replies
6.9k
views
I got low overall alignment rate running HiSAT2
RNA-Seq hisat hisat2 alignment
7.7 years ago by sslee1015 • 0
8
votes
14
replies
2.5k
views
6 follow
kallisto pseudoalignment rate is lower than literature
pseudoalignment kallisto RNA-seq
2.8 years ago by johnsonqinz • 0
8
votes
8
replies
1.9k
views
Sequence alignment algorithm for big size genes in MATLAB
alignment Matlab next-gen
7.0 years ago by r.tor ▴ 50
8
votes
11
replies
5.8k
views
RNASeq gender identification
RNA-Seq
6.7 years ago by popayekid55 ▴ 110
8
votes
4
replies
2.4k
views
Global Sequence Alignment
alignment
11.0 years ago by behrang • 0
8
votes
7
replies
5.9k
views
Download human 3 UTR FASTA file
genome
8.2 years ago by bharata1803 ▴ 560
8
votes
5
replies
3.6k
views
Is it possible to guess sequencing platform used based on a FASTQ/BAM file?
BAM FASTQ
updated 17 months ago by 43k • written 8.9 years ago by ▴ 60
8
votes
5
replies
848
views
Frustrated with DEA results
microarray differential-expression
updated 7 months ago by ★ 6.0k • written 7 months ago by • 0
8
votes
7
replies
3.9k
views
6 follow
Compatibility between my reference genome and GTF file
rna-seq hisat2 alignment reference genome
5.6 years ago by Batu ▴ 250
8
votes
8
replies
1.5k
views
microRNA-seq sequence lenght distribution after trimming
alignment rna-seq
5.3 years ago by szabo.marton ▴ 10
8
votes
7
replies
595
views
adjusting parameters in ViolinPlot did not work
single-cell
updated 3 months ago by 43k • written 3 months ago by ▴ 100
8
votes
25
replies
3.1k
views
construction of a database
sql noSQL neo4j database
updated 14 months ago by 43k • written 3.0 years ago by ▴ 20
8
votes
4
replies
15k
views
Use of if-else statement in snakemake rule
snakemake if-else python
updated 4.5 years ago by • 0 • written 6.8 years ago by ▴ 140
8
votes
5
replies
3.2k
views
7 follow
What is the best way to merge multiple fasta files containing contigs?
Assembly Anvi’o fasta
updated 5.3 years ago by 11k • written 5.3 years ago by • 0
8
votes
11
replies
3.6k
views
Semantic Similarity selection in REVIGO: which is better? many clusters or few?
go revigo gene ontology
6.5 years ago by Farbod ★ 3.4k
8
votes
8
replies
2.8k
views
Making chain files
Assembly genome alignment sequence
updated 4.8 years ago by 20 • written 4.8 years ago by ▴ 50
8
votes
7
replies
4.3k
views
ORF finder script
orf open reading frame bash shell sequencing
7.3 years ago by ahm3dhany ▴ 20
8
votes
11
replies
1.9k
views
Sending files to Galaxy
Galaxy fastq
7.6 years ago by statfa ▴ 760
8
votes
5
replies
1.7k
views
differential expression analysis with DESeq2 & edgeR
RNA-Seq
3.5 years ago by Rob ▴ 170
8
votes
20
replies
2.7k
views
Getting read depth for normal and tumour
R WGS vcf
5.1 years ago by zizigolu ★ 4.3k
8
votes
6
replies
5.7k
views
miRanda output meaning?
rna-seq
updated 7.0 years ago by 47k • written 7.0 years ago by ▴ 40
8
votes
7
replies
4.1k
views
Error with Bowtie 2
bowtie2 alignment
6.9 years ago by valerie ▴ 100
8
votes
5
replies
911
views
Why some genome assemblies don't have annotation?
genome assembly
5.1 years ago by 860101959 ▴ 10
8
votes
4
replies
2.0k
views
using different tools to identify differential exprssed genes
rna-seq RNA-Seq R
updated 19 months ago by 43k • written 8.7 years ago by ▴ 20
8
votes
6
replies
4.4k
views
Bwa Aln -Q 15 When To Use It? What Does It Do?
bwa trimming
updated 11.8 years ago by 100k • written 11.8 years ago by ▴ 640
8
votes
16
replies
1.4k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene next-gen
4.3 years ago by Chaimaa ▴ 260
8
votes
9
replies
1.5k
views
superimpose
discovery ds visualizer
2.9 years ago by Alex ▴ 20
8
votes
3
replies
3.4k
views
which tool is used for separating forward and reverse from paired end fastq
Assembly
6.8 years ago by ranjini.shakthi • 0
8
votes
11
replies
4.1k
views
STAR can not detect this chimeric read
RNA-Seq fusion STAR
updated 7.5 years ago by 20 • written 7.7 years ago by 11k
8
votes
6
replies
1.3k
views
How to apply bioinformatic in vaccine design?
Vaccine
updated 18 months ago by ★ 2.5k • written 18 months ago by ▴ 50
8
votes
20
replies
2.5k
views
Converting runpsipred Script to Work on Windows OS
psipred windows
updated 24 months ago by 43k • written 5.8 years ago by ▴ 270
8
votes
10
replies
2.0k
views
FASTA of translated amino acid sequences in their six reading frames, which one is the optimal?
aminoacid protein peptide Reading optimal frames
2.8 years ago by Luis999 ▴ 20
8
votes
6
replies
948
views
How to create a Venn Diagram for overlapping SVs from a merged VCF
truvari structural-variants r vcf venn-diagram
6 months ago by Matteo Ungaro ▴ 100
8
votes
9
replies
3.1k
views
error in rstudio
csv matrix rstudio
updated 19 months ago by 43k • written 8.7 years ago by ★ 4.3k
8
votes
4
replies
3.2k
views
How to use machine learning in Fastq/Fasta data?
machine learning fasta fastq sequencing
7.0 years ago by inkprs ▴ 70
8
votes
14
replies
2.6k
views
RNA-Seq analysis with standard p-value
RNA-Seq
7.3 years ago by #### ▴ 220
8
votes
4
replies
2.2k
views
Use Of Terms In Genome-Wide Analysis: Phenotype / Functionality / Fitness
12.8 years ago by 2184687-1231-83- ★ 5.1k
1,000 results • Page 5 of 20
Recent Votes
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
A: Best de novo assembler for insect genome ?
Comment: sci-RNA-seq
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
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Recent Replies
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Prawesh • 0
thanks, it's working now.
Comment: Genome Visualization Tools by GenoMax 142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file by Trivas ★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R by jared.andrews07 ★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran by GenoMax 142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content by noodle ▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file? by wyuan37 • 0
Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file? by wyuan37 • 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses by LauferVA 4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data by GenoMax 142k
You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file by ramiro.barrantes • 0
Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
Answer: RNAseq RNA content by ntsopoul ▴ 60
I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
Comment: RNAseq RNA content by ATpoint 82k
What is "row RNA"?
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