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1,000 results • Page 2 of 20
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7
votes
7
replies
1.2k
views
Nextflow rnaseq finishing early
RNA-seq nextflow
updated 6 months ago by 40k • written 6 months ago by ★ 1.4k
7
votes
16
replies
2.4k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq sequencing
updated 6 months ago by 40k • written 6.0 years ago by ★ 3.6k
7
votes
8
replies
2.6k
views
Discrepency between number of reads tophat
RNA-Seq tophat software-error
updated 12 months ago by 40k • written 8.1 years ago by ▴ 380
7
votes
9
replies
1.0k
views
Tools to check the length of isoforms in reference transcript
transcript histogram isoform
11 months ago by Jjbox ▴ 40
7
votes
3
replies
1.2k
views
Using a Docker image with ensembl-vep
Linux ensembl-vep Docker
updated 9 months ago by ★ 1.8k • written 9 months ago by ▴ 50
7
votes
4
replies
4.1k
views
IGV genome browser problems
igv
updated 9 months ago by 40k • written 8.2 years ago by ▴ 210
6
votes
3
replies
1.8k
views
Gene network with expression data
network RNA-Seq
updated 3 months ago by 40k • written 5.8 years ago by ▴ 30
6
votes
7
replies
1.5k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters Algorithm Software
updated 4 months ago by 40k • written 6.3 years ago by ▴ 90
6
votes
2
replies
589
views
miRNA tool for search targets for genes
mirna targets
updated 3 months ago by 40k • written 2.2 years ago by ★ 1.2k
6
votes
7
replies
962
views
to mark the duplicates
Assembly
updated 6 months ago by 40k • written 4.3 years ago by ▴ 10
6
votes
7
replies
4.3k
views
8 follow
desktop bioinformatics platform specs
hardware desktop
updated 9 months ago by 40k • written 8.3 years ago by ▴ 610
6
votes
6
replies
3.6k
views
Already Working In The Field Of Bioinformatics With A Bachelors, Is A Masters Degree Worth The Time?
masters career
updated 7 months ago by 40k • written 10.0 years ago by ▴ 30
6
votes
9
replies
1.4k
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM Bowtie
updated 4 months ago by 40k • written 8 months ago by ▴ 50
6
votes
3
replies
3.2k
views
Comment On The Introduction Of A Bioinformatics Paper
publication bayesian-model
updated 6 months ago by 40k • written 9.5 years ago by ▴ 210
6
votes
4
replies
578
views
Equivalent to SeqMan alignment tool
SeqMan alignments
7 months ago by A_heath ▴ 140
6
votes
9
replies
2.4k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool Cellranger NCBI
updated 3 months ago by 40k • written 20 months ago by ▴ 20
6
votes
3
replies
544
views
trimmomatic and STAR alignments
trimmomatic STAR RNAseq sequencing reads
updated 4 months ago by ▴ 140 • written 5 months ago by ▴ 20
6
votes
6
replies
2.9k
views
ChIP-Seq Intensity Analysis
R ChIP-Seq
updated 4 months ago by 40k • written 5.8 years ago by ▴ 20
6
votes
4
replies
519
views
Tools for strand direction detection RNA-Seq
Rna-seq strandedness
updated 10 months ago by 6.1k • written 10 months ago by ▴ 40
6
votes
2
replies
2.4k
views
Which is the best smoothing technique for replacing zeros from data?
Smoothing
updated 8 months ago by 40k • written 8.3 years ago by ★ 4.2k
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 40k • written 4.7 years ago by ▴ 290
6
votes
3
replies
312
views
Optimal Over Representation Analysis DE genes foldFC threshold?
ClusterProfiler ORA EnrichGo DGE
updated 9 weeks ago by 3.7k • written 9 weeks ago by ▴ 100
6
votes
12
replies
967
views
Help with error in cellranger
Cellranger
updated 4 months ago by 134k • written 4 months ago by ▴ 180
6
votes
13
replies
1.1k
views
Error with STAR
STAR
updated 6 months ago by 40k • written 6 months ago by ▴ 180
6
votes
1
reply
285
views
16S vs shotgun tools
metagenomics
8 weeks ago by anasjamshed ▴ 120
6
votes
7
replies
1.5k
views
Reference genome for RNA-Seq reads decontamination
FastQ_Screen RNA-Seq
updated 4 weeks ago by 40k • written 3.5 years ago by ▴ 60
6
votes
2
replies
562
views
Need to Modify this
language R
updated 9 months ago by 77k • written 9 months ago by • 0
6
votes
6
replies
4.4k
views
Performance of circRNA detection tools
RNA-Seq circRNA
updated 11 months ago by 40k • written 8.2 years ago by ▴ 240
6
votes
7
replies
1.2k
views
The size of the genome in pb of an organism before sequencing?
sequencing genome
updated 6 months ago by 40k • written 4.9 years ago by • 0
6
votes
9
replies
5.0k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 6 months ago by 40k • written 8.5 years ago by ▴ 10
6
votes
7
replies
4.6k
views
Creation Of A .Bed File From .Txt
plink
updated 6 months ago by 40k • written 9.7 years ago by • 0
6
votes
6
replies
1.1k
views
RNA-seq pipeline for degraded RNA
RNA-Seq degraded pipeline alignment
updated 6 months ago by ▴ 80 • written 2.7 years ago by ▴ 60
6
votes
11
replies
1.2k
views
Calculate RPKM
RPKM
6 months ago by Chris ▴ 180
6
votes
2
replies
669
views
Can the input file name be the same as the output file in `samtools sort`?
Samtools
updated 3 months ago by 40k • written 19 months ago by ▴ 140
6
votes
6
replies
1.3k
views
paired read or not paired read
RNA-Seq
updated 9 months ago by 40k • written 8.4 years ago by ★ 4.2k
6
votes
5
replies
5.1k
views
MA plots DESeq: strange MA plots
RNA-Seq MAplot DESeq
updated 9 months ago by 40k • written 8.2 years ago by ★ 1.1k
6
votes
1
reply
2.0k
views
gene expression in bioinformatics
gene-expression
updated 12 months ago by 40k • written 8.1 years ago by • 0
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 40k • written 3.1 years ago by ▴ 20
6
votes
6
replies
4.6k
views
MSD calculations vs time
MDsimulation python computational-biology
updated 9 months ago by 40k • written 8.2 years ago by ▴ 30
5
votes
6
replies
694
views
error: Couldn't open trackDb.txt in hubCheck
UCSC hubCheck
updated 10 months ago by 11k • written 10 months ago by ▴ 320
5
votes
10
replies
602
views
Error when viewing a bam file
samtools
updated 3 months ago by 40k • written 4 months ago by ▴ 180
5
votes
1
reply
3.7k
views
Sample clustering in RNASeq
deseq2 RNASeq heatmap
updated 12 months ago by 40k • written 8.1 years ago by ▴ 120
5
votes
2
replies
657
views
how to loop through various dataframes in R
dataframe R
updated 8 months ago by 11k • written 9 months ago by ▴ 140
5
votes
5
replies
3.4k
views
Gencode annotation and read counting- how to handle overlapping/ambiguous features
gencode alignment RNA-Seq
updated 9 months ago by 40k • written 8.3 years ago by ▴ 680
5
votes
6
replies
1.9k
views
check duplicates in two columns
ChIP-Seq sequencing SNP
updated 9 months ago by 40k • written 8.3 years ago by • 0
5
votes
4
replies
3.8k
views
Black color reads in IGV: bwa-meth
IGV alignment bwa-meth
updated 8 months ago by 40k • written 8.3 years ago by ▴ 220
5
votes
8
replies
664
views
conda: command not found: gatk.
conda gatk
3 months ago by bestone ▴ 20
5
votes
7
replies
539
views
About the value in bigwig file
ATAC-seq
updated 11 weeks ago by ▴ 810 • written 12 weeks ago by ▴ 180
5
votes
6
replies
1.2k
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
samtools bam bed
updated 3 months ago by 40k • written 10 months ago by ▴ 350
5
votes
2
replies
2.9k
views
Cut & run - bowtie2 dovetail option
cut and run dovetail bowtie2
updated 8 months ago by • 0 • written 2.9 years ago by ▴ 280
1,000 results • Page 2 of 20
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Recent Replies
Comment: Network analysis with cytoscape by Chris ▴ 180
Sure, the network represents the different expressed genes in my RNA-seq. I choosed string protein query.
Comment: Network analysis with cytoscape by Yogi ▴ 40
A few questions. 1. What does the network represent? 2. Can you insert a high level picture of the network (or pictures) if you want to zo…
Answer: Chip-Seq and correlation of bam file by jared.andrews07 ★ 15k
Use [deepTools' plotCorrelation function](https://deeptools.readthedocs.io/en/develop/content/tools/plotCorrelation.html).
Answer: Transcription factor co-localization p-values by jared.andrews07 ★ 15k
[regioneR](https://bioconductor.org/packages/release/bioc/html/regioneR.html) seems to be what you want.
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data by LChart 3.4k
> Our major biological questions are: to have a general comparison of cancer vs normal “treatment” conditions; In addition if doable, to co…
Comment: Which function is best for pathway analysis? by Chris ▴ 180
Thanks @luffy! Great material but seem they didn't mention how to customize the background genes depend on our data.
Comment: CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM by camillab. ▴ 140
I have calculate from this [tutorial][1]. so basically it retrieve the normalized counts matrix using `Deseq2` . Do you think it is correct…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by GenoMax 134k
`dorado` can't demultiplex data as yet (v.0.3.4). Also no adapter trimming. So something to keep in mind if you are switching. To address …
Comment: Frustrated with DEA results by dsull ★ 4.7k
Let the data speak. If there's no difference, then there's no difference. Human clinical data is always messy and unpredictable, especiall…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by Ram 40k
I don't think they bought the Mac Studio just for the MiniON. If they did, that might be overkill. All things considered, I'd prefer an App…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by ATpoint 77k
Wondering why investing all that money for such an overpriced piece of hardware. You could get an equivalent Windows or Linux workstation f…
Answer: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by Christopher ▴ 10
I'm using a Mac Studio with M1 Ultra chip to sequence with a MinION Mk1B now and it's working great! Fast basecalling and adaptive sequenci…
Comment: ncbi error report log for validate fastq issue by GenoMax 134k
You may want to use `--split-files` instead. With your `--split-spot` option looks like you end up with interleaved data files. Unless you …
Comment: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor by Ram 40k
Nope, I kinda gave up. I got to the image on what fragment size is (https://www.biostars.org/p/106291/#106344) but cannot figure out how to…
Comment: ncbi error report log for validate fastq issue by 1769mkc ★ 1.1k
I got it working after i updated the sra lite option while using vdb-config -i the output is what i see like this docker run -t -…
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