Limit : all time
all time today this week this month this year
1,000 results • Page 6 of 20
Sort: Votes
Rank Views Votes Replies
8
votes
11
replies
2.0k
views
using STAR instead of HISAT2
STAR
updated 22 months ago by 43k • written 22 months ago by ▴ 280
7
votes
10
replies
3.8k
views
How to use Ray and BBmap to generate metagenome co-assembly
Ray BBmap assembly
updated 8.0 years ago by 142k • written 8.0 years ago by ▴ 130
7
votes
4
replies
7.0k
views
Which genome files to use for STAR?
alignment star genome
5.0 years ago by Nico80 ▴ 80
7
votes
10
replies
865
views
New insights from old data?
genome rna-seq sequence
4.2 years ago by schlogl ▴ 160
7
votes
5
replies
1.7k
views
RNAseq uneven PCR bias "how to take into best take into account uneven PCR bias ?"
RNA-Seq rna-seq
updated 6.5 years ago by 20 • written 6.6 years ago by • 0
7
votes
4
replies
3.6k
views
Abra for indel realignment
realignment abra gatk
updated 2.2 years ago by 43k • written 9.4 years ago by ▴ 640
7
votes
8
replies
1.7k
views
fastq dump usage of microRNA-seq data
RNA-Seq microRNA fastq
5.0 years ago by K.patel5 ▴ 140
7
votes
1
reply
7.0k
views
createRepeatLandscape in RepeatMasker
RepeatMasker
7.7 years ago by a.rex ▴ 350
7
votes
8
replies
2.9k
views
Discrepency between number of reads tophat
RNA-Seq tophat software-error
updated 19 months ago by 43k • written 8.7 years ago by ▴ 380
7
votes
4
replies
2.0k
views
Transcriptome analysis using tophat and bowtie
tophat bowtie BowtieIndex software error
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
7
votes
5
replies
3.3k
views
Demultiplex fastq files in which barcodes and primers are already removed
RNA-Seq 16S Demultiplex
7.4 years ago by kapuriakaran • 0
7
votes
3
replies
5.5k
views
Ensemble Identifier Of Mirna
mirna gene-ontology enrichment analysis bioinformatician microarray
10.5 years ago by khan ▴ 100
7
votes
9
replies
1.2k
views
Find a gene from RNA-seq data without GTF
RNA-Seq
4.2 years ago by avino ▴ 20
7
votes
19
replies
3.0k
views
mapping script process sleeping on server.
alignment
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 30
7
votes
14
replies
1.5k
views
How to Blast with multiple species - Phylogenetic Analysis
ChIP-Seq alignment sequence
4.0 years ago by dimitrischat ▴ 210
7
votes
14
replies
5.0k
views
How to Calulate Allele Frequency from a VCF File?
frequency allele VCF
updated 15 months ago by 22k • written 15 months ago by ▴ 10
7
votes
6
replies
4.6k
views
What's the real difference between these two types of methods for assessing differential expression?
RNA-Seq differential-expression methods
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 60
7
votes
14
replies
2.1k
views
single-cell exome sequencing pipeline
SNP exom single-cell next-gen
7.6 years ago by zizigolu ★ 4.3k
7
votes
10
replies
3.9k
views
Choosing phylogenetic approaches
phylogeny
updated 2.3 years ago by 43k • written 9.7 years ago by ▴ 110
7
votes
9
replies
4.6k
views
Alignment in IGV: extracting specific reads.
iGV samtools
6.5 years ago by KVC_bioinfo ▴ 590
7
votes
7
replies
3.1k
views
kmers in rna-seq
RNA-Seq kmer
updated 2.4 years ago by 43k • written 9.8 years ago by ▴ 130
7
votes
7
replies
1.4k
views
Machine learning with whole genome sequence data in cancer research?
cancer genome
5.7 years ago by dan ▴ 20
7
votes
15
replies
4.3k
views
Biopython Pairwise Alignment output
biopython needleman global alignment
4.1 years ago by tommaso.green • 0
7
votes
12
replies
3.3k
views
RNA secondary structure - Feature extraction
RNA secondary structure Structural Fragments
6.0 years ago by Manu Madhavan ▴ 20
7
votes
4
replies
2.8k
views
Removing a chromosome from a fasta file
fasta chromosome sequence
6.1 years ago by t86dan ▴ 30
7
votes
3
replies
2.1k
views
dbSNP vcf file is corrupted?
vcf gunzip dbSNP
3.0 years ago by HB ▴ 30
7
votes
11
replies
1.8k
views
Strandness setting for HISAT2 : BGI sequencing platform
RNA-Seq Hisat2
updated 3.6 years ago by 142k • written 3.6 years ago by ▴ 70
7
votes
0
replies
2.9k
views
Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search
search alignment
10.4 years ago by Rob 6.6k
7
votes
14
replies
4.0k
views
Bowtie2 throws error no. 139
bowtie2 ngs alignment software error sequencing
7.2 years ago by anu014 ▴ 190
7
votes
7
replies
1.5k
views
GSEA analysis
Hi
updated 2.1 years ago by ▴ 10 • written 2.1 years ago by ▴ 10
7
votes
4
replies
2.7k
views
RSEM BAM outputs, which one to use for RSeQC?
RSEM STAR RSeQC BAM
2.1 years ago by Freek ▴ 60
7
votes
3
replies
2.4k
views
Is It Possible To Perform Synteny Study Between A Transcriptome And Genome Of Closely Related Species?
snp transcriptome
updated 10.3 years ago by 100k • written 10.3 years ago by ▴ 120
7
votes
4
replies
923
views
How to extract variants falling in a genomic window from a VCF?
vcf
updated 2.9 years ago by 142k • written 2.9 years ago by ▴ 80
7
votes
16
replies
21k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
7.8 years ago by aggregatibacter ▴ 180
7
votes
9
replies
2.3k
views
statistical analysis of RNA-seq
RNA-Seq Statistics
7.6 years ago by statfa ▴ 760
7
votes
2
replies
5.3k
views
Store Structural Variants Into Vcf
vcf
11.2 years ago by Tomáš Beluský ▴ 90
7
votes
7
replies
1.8k
views
Nextflow rnaseq finishing early
RNA-seq nextflow
updated 13 months ago by 43k • written 13 months ago by ★ 1.4k
7
votes
14
replies
6.0k
views
transcriptome index for Kalisto
RNA-Seq
updated 7.3 years ago by 20 • written 7.5 years ago by ★ 1.2k
7
votes
18
replies
8.6k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 2.3 years ago by 43k • written 9.5 years ago by ▴ 190
7
votes
4
replies
2.2k
views
Error: missing values and NaN's not allowed if 'na.rm' is FALSE
Genome Software
22 months ago by sunnykevin97 ▴ 980
7
votes
13
replies
4.5k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq trimming fastqc
updated 6 months ago by 82k • written 3.5 years ago by ▴ 10
7
votes
17
replies
6.6k
views
HeatMap: how to cluster only the rows and keep order of the heatmap's column labels as same as in the df?
R gene genome
5.9 years ago by WUSCHEL ▴ 760
7
votes
29
replies
2.5k
views
What's the powerful biological methods for significant genes selection?
gene selection significant biological method R
5.5 years ago by Chaimaa ▴ 260
7
votes
2
replies
2.4k
views
Trying to reproduce mirbase results locally with BLAST
blast
6.5 years ago by avino ▴ 20
7
votes
5
replies
5.6k
views
How to know if it is 'one-color' or 'two-color' microarray?
microarray RNA-Seq ChIP-Seq sequencing
7.6 years ago by learnBioinformatics ▴ 60
7
votes
7
replies
1.5k
views
Am I unnecessarily 'missing' a high number of true-positive DE genes? Or do I just not understand the statistics?
RNA-Seq R edgeR
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 370
7
votes
9
replies
6.6k
views
Converting Gene Predictions In Glimmer To Protein Sequences.
script biopython
updated 2.3 years ago by 43k • written 10.8 years ago by ▴ 50
7
votes
5
replies
4.0k
views
Trinity de novo transcript assembly too many transcripts
RNA-Seq Assembly
updated 21 months ago by 43k • written 8.9 years ago by ▴ 820
7
votes
3
replies
1.6k
views
What are the best tools for Genome assembly
Assembly genome
updated 11 months ago by 43k • written 5.8 years ago by ▴ 10
7
votes
12
replies
2.6k
views
Is this variant probably an artifact?
VCF Exome Sequencing
6.2 years ago by Sharon ▴ 610
1,000 results • Page 6 of 20
Recent Votes
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
Recent Locations • All
Belgium, just now
São Paulo, 2 minutes ago
Italy, 5 minutes ago
France/Nantes/Institut du Thorax - INSERM UMR1087, 5 minutes ago
Hong Kong, 7 minutes ago
China, 13 minutes ago
India, 18 minutes ago
Recent Awards • All
Popular Question to syedahamdani94 • 0
Popular Question to mohammadhassanj ▴ 260
Scholar to dsull ★ 6.0k
Popular Question to finswimmer 16k
Popular Question to Ezequiel • 0
Popular Question to alanh ▴ 170
Scholar to Peter 6.0k
Recent Replies
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Traffic: 1375 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6