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1,000 results • Page 2 of 20
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7
votes
10
replies
1.5k
views
col as names [solved]
R
updated 8 months ago by 41k • written 4.7 years ago by ▴ 100
7
votes
4
replies
1.4k
views
So many Zeros (read counting)_NGS sequence analysis with R / Bioconductor: RNA-Seq workflow
alignment RNA-Seq R
updated 8 months ago by 41k • written 5.4 years ago by • 0
7
votes
6
replies
1.1k
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 6 months ago by 78k • written 6 months ago by ▴ 190
7
votes
8
replies
1.8k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock gene-duplication phylogeny
updated 10 months ago by 41k • written 8.6 years ago by ▴ 20
7
votes
7
replies
1.5k
views
Nextflow rnaseq finishing early
RNA-seq nextflow
updated 8 months ago by 41k • written 8 months ago by ★ 1.4k
6
votes
3
replies
1.9k
views
Gene network with expression data
network RNA-Seq
updated 5 months ago by 41k • written 6.0 years ago by ▴ 30
6
votes
9
replies
5.1k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 8 months ago by 41k • written 8.6 years ago by ▴ 10
6
votes
6
replies
3.0k
views
ChIP-Seq Intensity Analysis
R ChIP-Seq
updated 6 months ago by 41k • written 6.0 years ago by ▴ 20
6
votes
2
replies
714
views
Can the input file name be the same as the output file in `samtools sort`?
Samtools
updated 5 months ago by 41k • written 21 months ago by ▴ 160
6
votes
12
replies
1.3k
views
Help with error in cellranger
Cellranger
updated 6 months ago by 136k • written 6 months ago by ▴ 230
6
votes
1
reply
346
views
16S vs shotgun tools
metagenomics
4 months ago by anasjamshed ▴ 120
6
votes
6
replies
3.7k
views
Already Working In The Field Of Bioinformatics With A Bachelors, Is A Masters Degree Worth The Time?
masters career
updated 9 months ago by 41k • written 10.2 years ago by ▴ 30
6
votes
12
replies
1.4k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r biomarker
updated 8 months ago by 41k • written 4.9 years ago by ▴ 290
6
votes
3
replies
3.3k
views
Comment On The Introduction Of A Bioinformatics Paper
publication bayesian-model
updated 9 months ago by 41k • written 9.7 years ago by ▴ 210
6
votes
6
replies
1.3k
views
paired read or not paired read
RNA-Seq
updated 11 months ago by 41k • written 8.6 years ago by ★ 4.2k
6
votes
3
replies
393
views
Optimal Over Representation Analysis DE genes foldFC threshold?
ClusterProfiler ORA EnrichGo DGE
updated 4 months ago by 3.8k • written 4 months ago by ▴ 100
6
votes
9
replies
1.6k
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM Bowtie
updated 6 months ago by 41k • written 10 months ago by ▴ 50
6
votes
2
replies
625
views
miRNA tool for search targets for genes
mirna targets
updated 5 months ago by 41k • written 2.4 years ago by ★ 1.2k
6
votes
13
replies
1.3k
views
Error with STAR
STAR
updated 9 months ago by 41k • written 9 months ago by ▴ 230
6
votes
7
replies
1.5k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters Algorithm Software
updated 6 months ago by 41k • written 6.5 years ago by ▴ 90
6
votes
3
replies
260
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics box-plot R scale_adjustment logarithm
updated 6 days ago by ▴ 860 • written 6 days ago by ▴ 40
6
votes
11
replies
1.4k
views
Calculate RPKM
RPKM
8 months ago by Chris ▴ 230
6
votes
9
replies
2.6k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool Cellranger NCBI
updated 5 months ago by 41k • written 23 months ago by ▴ 20
6
votes
7
replies
1.3k
views
The size of the genome in pb of an organism before sequencing?
sequencing genome
updated 8 months ago by 41k • written 5.1 years ago by • 0
6
votes
7
replies
1.6k
views
Reference genome for RNA-Seq reads decontamination
FastQ_Screen RNA-Seq
updated 3 months ago by 41k • written 3.7 years ago by ▴ 60
6
votes
4
replies
662
views
Equivalent to SeqMan alignment tool
SeqMan alignments
10 months ago by A_heath ▴ 160
6
votes
3
replies
627
views
trimmomatic and STAR alignments
trimmomatic STAR RNAseq sequencing reads
updated 7 months ago by ▴ 140 • written 8 months ago by ▴ 40
6
votes
7
replies
4.7k
views
Creation Of A .Bed File From .Txt
plink
updated 8 months ago by 41k • written 9.8 years ago by • 0
6
votes
12
replies
1.5k
views
VCF files 101 - for people from non Bioinformatics Background
vcf sequencing genome variant-calling
updated 8 months ago by 41k • written 3.3 years ago by ▴ 20
6
votes
7
replies
1.0k
views
to mark the duplicates
Assembly
updated 8 months ago by 41k • written 4.5 years ago by ▴ 10
6
votes
2
replies
2.4k
views
Which is the best smoothing technique for replacing zeros from data?
Smoothing
updated 11 months ago by 41k • written 8.5 years ago by ★ 4.2k
6
votes
7
replies
4.4k
views
8 follow
desktop bioinformatics platform specs
hardware desktop
updated 11 months ago by 41k • written 8.5 years ago by ▴ 610
6
votes
2
replies
605
views
Need to Modify this
language R
updated 11 months ago by 78k • written 11 months ago by • 0
6
votes
6
replies
1.2k
views
RNA-seq pipeline for degraded RNA
RNA-Seq degraded pipeline alignment
updated 9 months ago by ▴ 80 • written 2.9 years ago by ▴ 60
5
votes
14
replies
3.7k
views
How to Calulate Allele Frequency from a VCF File?
frequency allele VCF
updated 10 months ago by 22k • written 10 months ago by • 0
5
votes
6
replies
3.2k
views
Changes log2FC values of DESeq2
log2FC DESeq2
updated 8 months ago by 41k • written 6.0 years ago by ▴ 30
5
votes
4
replies
1.6k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection DE-genes multi-treatments time-series
updated 6 months ago by 41k • written 7.4 years ago by ▴ 740
5
votes
3
replies
709
views
GENE code ID conversion
ensembl entrez
8 months ago by Confused_human ▴ 20
5
votes
10
replies
945
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR RNA-seq
3 months ago by alwayshope ▴ 40
5
votes
6
replies
3.2k
views
Can't access DAVID
DAVID
updated 11 months ago by 41k • written 8.4 years ago by ★ 4.1k
5
votes
8
replies
1.8k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq DNA-Seq contamination QC
updated 7 weeks ago by • 0 • written 3.3 years ago by ▴ 230
5
votes
8
replies
1.3k
views
snpeff install error
snpeff
updated 6 months ago by 41k • written 7 months ago by ▴ 20
5
votes
12
replies
1.0k
views
Data from an experiment
single-cell
updated 9 months ago by 136k • written 9 months ago by ▴ 230
5
votes
6
replies
1.3k
views
DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
DESeq2 R RNA-Seq
updated 5 months ago by 41k • written 3.6 years ago by ▴ 90
5
votes
3
replies
910
views
abyss-pe genome assembly
konnector abyss-pe
updated 5 months ago by 41k • written 4.8 years ago by • 0
5
votes
4
replies
947
views
Converting Bam file to Fasta (Zipped)
bedtools samtools
updated 5 months ago by 41k • written 13 months ago by ▴ 350
5
votes
4
replies
1.8k
views
MyVariant.info fields descriptions?
genome snp variant
updated 8 months ago by 41k • written 7.6 years ago by ▴ 90
5
votes
4
replies
4.0k
views
Black color reads in IGV: bwa-meth
IGV alignment bwa-meth
updated 11 months ago by 41k • written 8.5 years ago by ▴ 220
5
votes
11
replies
733
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 3 months ago by 41k • written 4 months ago by ▴ 230
5
votes
6
replies
608
views
normalize coordinates to the same length
r genomicranges
8 months ago by Chironex ▴ 40
1,000 results • Page 2 of 20
Recent Votes
A: Compute mean depth coverage for exome data with paired end, overlapping, feature
C: Compute mean depth coverage for exome data with paired end, overlapping, feature
Answer: How to use Nextflow to call scripts from different environments?
Comment: An issue with gtf file (ballgownrsem)
Answer: how to calculate duplicated reads in single cell RNA 10x genomics data
What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
A: Understand Samtools View Output
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Comment: Need help to find FASTA sequence from dbSNP by syedahumairagillani • 0
Thank you for your response. Actually I am looking for fasta sequence of SNP as I shared via image, rather than just location. Would you p…
Answer: Calculate GC content for entire chromosome by colindaven 5.8k
In the meantime there is also seqtk gc https://github.com/lh3/seqtk seqtk gc Usage: seqtk gc [options] <in.fa> …
Comment: Building reference dbSNP file using WGS samples by analyst ▴ 10
I have employed your above suggested approach for BQSR (latter one). I will try former approach too (that does not require reference vcf fi…
Comment: An issue with gtf file (ballgownrsem) by cucindarko51 • 0
Thank you! After using this tool, I figured out that **ballgownrsem** can be run successfully only with GFF files.
Answer: Execute R command on specific termimal by ATpoint 78k
This is not how HPCs work. Things do not happen automatically and independent of the job scheduler. If you want to work interactively o…
Comment: Need help to find FASTA sequence from dbSNP by GenoMax 136k
Using [**EntrezDirect**][1] you can find the location of this SNP: $ esearch -db snp -query rs1815739 | esummary | xtract -pattern Doc…
Comment: Building reference dbSNP file using WGS samples by analyst ▴ 10
For variant calling I followed following steps: **Step 1** I first made a vcf file to be used for quality score recalibration later > c…
Comment: Need help to find FASTA sequence from dbSNP by Pierre Lindenbaum 158k
what does it mean ?
Answer: How to use Nextflow to call scripts from different environments? by ATpoint 78k
You can specify conda environments and containers directly in the modules, see for example: https://github.com/nf-core/modules/blob/master…
Comment: Issues while running blastx by GenoMax 136k
> ~/Downloads/uniprot_sprot.dat `dat` files are not blast index ready. You should download the `fasta` format file and create your own bla…
Comment: Strandedness of RNA-seq results by charles.feigin • 0
Hi, coming here for the same reason. Libraries prepared with the Illumina Stranded mRNA Prep kit (dUTP-based). In hisat2 with --rf I get <…
Comment: How to interpret the discrepancy of assignment rate in featurecounts using forwa by charles.feigin • 0
I'm having this exact same problem. PolyA RNA-Seq library, running with --fr in hisat2 gives a high fraction of concordant single-mappers, …
Comment: How to create a mutation frequency comparison plot? by saipra003 ▴ 10
That's awesome thank you. Found out after a bit of researching that this is called a `Cleveland Dot Plot` if anyone else comes across this.
Comment: Cell ranger multi for demultiplexing FB files and GEX files by GenoMax 136k
Demultiplexing is typically done using Illumina software? Have you done this already?: https://www.10xgenomics.com/support/software/cell-ra…
Comment: bbmap split paired-end reads back into separated fastq files? by GenoMax 136k
If you simply want to merge "technical" sequencing replicates then you can do the following cat file1_R1.fastq file1_R1.fastq > merged…
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