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1,000 results • Page 2 of 20
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7
votes
4
replies
4.0k
views
IGV genome browser problems
igv
updated 5 months ago by 39k • written 7.9 years ago by ▴ 210
7
votes
7
replies
1.5k
views
LRT test with DESeq2 and how to interpret the results
significant LRT DESeq2 genes RNA-Seq
updated 10 months ago by ★ 1.1k • written 12 months ago by ▴ 20
7
votes
9
replies
863
views
Tools to check the length of isoforms in reference transcript
transcript histogram isoform
7 months ago by Jjbox ▴ 40
7
votes
3
replies
736
views
Using a Docker image with ensembl-vep
Linux ensembl-vep Docker
updated 5 months ago by ★ 1.5k • written 5 months ago by ▴ 30
7
votes
5
replies
2.2k
views
using machine learning regards to ribo-seq data sets
gene-regulatory-network ribo-seq machine-learning
updated 7 months ago by 39k • written 7.8 years ago by ★ 4.2k
7
votes
16
replies
2.1k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq sequencing
updated 9 weeks ago by 39k • written 5.6 years ago by ★ 3.6k
7
votes
7
replies
4.3k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines DESeq2 time-series RNA-Seq
updated 6 hours ago by 39k • written 4.4 years ago by ▴ 80
7
votes
10
replies
1.3k
views
Ubuntu 20.04 Crash
Ubuntu
updated 3 months ago by 39k • written 16 months ago by • 0
7
votes
8
replies
3.4k
views
remove duplicated entries from BLAST result file
blast alignment
updated 5 months ago by 39k • written 8.0 years ago by ▴ 160
7
votes
4
replies
2.9k
views
Mapping BAM/SAM file back to reference?!?!
SAM reference BWA BAM
updated 8 months ago by 39k • written 7.6 years ago by ▴ 50
7
votes
7
replies
794
views
Nextflow rnaseq finishing early
RNA-seq nextflow
updated 9 weeks ago by 39k • written 9 weeks ago by ★ 1.4k
7
votes
4
replies
1.8k
views
useful and freely available softwares for Bioinformatics
software
updated 10 weeks ago by 39k • written 8.2 years ago by ▴ 920
7
votes
8
replies
3.2k
views
DEseq2 design matrix with 3 factors
rna-seq deseq2 Forum
updated 11 months ago by ★ 1.1k • written 3.0 years ago by ▴ 60
7
votes
5
replies
3.7k
views
Trinity de novo transcript assembly too many transcripts
RNA-Seq Assembly
updated 10 months ago by 39k • written 8.0 years ago by ▴ 800
6
votes
7
replies
2.3k
views
Standardizing the language of lab protocols [Current status]
protocols automation
updated 8 months ago by 39k • written 7.7 years ago by ▴ 20
6
votes
7
replies
5.9k
views
best alignment tool for Ion Torrent data
chloroplast genome iontorrent
updated 9 months ago by 39k • written 7.5 years ago by ★ 2.3k
6
votes
7
replies
1.1k
views
The size of the genome in pb of an organism before sequencing?
sequencing genome
updated 9 weeks ago by 39k • written 4.6 years ago by • 0
6
votes
6
replies
4.5k
views
MSD calculations vs time
MDsimulation python computational-biology
updated 5 months ago by 39k • written 7.9 years ago by ▴ 30
6
votes
13
replies
6.0k
views
DESeq2 and edgeR - no agreement between results
RNA-Seq edgeR DESeq2
updated 9 months ago by 39k • written 7.5 years ago by ▴ 60
6
votes
6
replies
1.2k
views
paired read or not paired read
RNA-Seq
updated 5 months ago by 39k • written 8.1 years ago by ★ 4.2k
6
votes
14
replies
2.7k
views
mapping RNAseq reads to a genbank isoforme that is not in Reference Annotation
RNA-Seq sequence cufflinks new isoform in rnaseq
updated 10 months ago by 39k • written 7.3 years ago by • 0
6
votes
10
replies
889
views
Understanding bam tracks
RNA sequencing bam
updated 8 months ago by 154k • written 8 months ago by ▴ 30
6
votes
6
replies
4.3k
views
Performance of circRNA detection tools
RNA-Seq circRNA
updated 7 months ago by 39k • written 7.8 years ago by ▴ 240
6
votes
6
replies
960
views
RNA-seq pipeline for degraded RNA
RNA-Seq degraded pipeline alignment
updated 12 weeks ago by ▴ 80 • written 2.3 years ago by ▴ 60
6
votes
3
replies
1.7k
views
PLINK results interpretation
SNP software-error
updated 8 months ago by 39k • written 7.9 years ago by ▴ 40
6
votes
5
replies
1.8k
views
the gene_id column is different for each sample when counting fpkm in galaxy cufflinks
RNA-Seq galaxy cufflinks fpkm
updated 10 months ago by 39k • written 7.5 years ago by ★ 4.2k
6
votes
4
replies
2.5k
views
Trouble renaming output files after running PHYLIP programs from a BASH script
PHYLIP sequence software-error
updated 10 months ago by 39k • written 7.4 years ago by ▴ 880
6
votes
6
replies
540
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 11 days ago by 72k • written 12 days ago by ▴ 120
6
votes
2
replies
1.7k
views
Periodicity in SNP calling quality - is this normal?
RNA-Seq VCF GATK SNP
updated 8 months ago by 39k • written 7.7 years ago by 13k
6
votes
7
replies
875
views
to mark the duplicates
Assembly
updated 11 weeks ago by 39k • written 4.0 years ago by ▴ 10
6
votes
15
replies
1.0k
views
The Best Cloud Solution For Genomics
cloud data-sharing genomics workflow
updated 10 months ago by 39k • written 11 months ago by ▴ 50
6
votes
9
replies
1.2k
views
for paired-end unmapped reads after star mapping
STAR-mapping Trinity assembly unmapped-reads
updated 9 months ago by 129k • written 9 months ago by • 0
6
votes
5
replies
5.0k
views
MA plots DESeq: strange MA plots
RNA-Seq MAplot DESeq
updated 5 months ago by 39k • written 7.9 years ago by ★ 1.1k
6
votes
4
replies
425
views
Tools for strand direction detection RNA-Seq
Rna-seq strandedness
updated 6 months ago by 6.0k • written 6 months ago by ▴ 40
6
votes
2
replies
4.3k
views
Adding header to VCF and combine VCF
vcf
updated 10 months ago by 39k • written 7.6 years ago by ▴ 40
6
votes
3
replies
393
views
trimmomatic and STAR alignments
trimmomatic STAR RNAseq sequencing reads
updated 26 days ago by ▴ 140 • written 7 weeks ago by ▴ 20
6
votes
6
replies
3.2k
views
Bowtie2 classification of discordantly mapped pairs
discordant-pairs bowtie2 alignment
updated 8 months ago by 39k • written 7.7 years ago by ▴ 30
6
votes
2
replies
2.3k
views
Which is the best smoothing technique for replacing zeros from data?
Smoothing
updated 4 months ago by 39k • written 8.0 years ago by ★ 4.2k
6
votes
13
replies
791
views
Error with STAR
STAR
updated 11 weeks ago by 39k • written 12 weeks ago by ▴ 100
6
votes
1
reply
2.0k
views
gene expression in bioinformatics
gene-expression
updated 8 months ago by 39k • written 7.8 years ago by • 0
6
votes
9
replies
4.8k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 10 weeks ago by 39k • written 8.1 years ago by ▴ 10
6
votes
6
replies
2.6k
views
ChIP-Seq Intensity Analysis
R ChIP-Seq
updated 13 days ago by 39k • written 5.5 years ago by ▴ 20
6
votes
3
replies
2.1k
views
vcf-merge gives empty output or run forever
vcf-merge vcftools
updated 10 months ago by 39k • written 7.3 years ago by • 0
6
votes
2
replies
492
views
Need to Modify this
language R
updated 5 months ago by 72k • written 5 months ago by • 0
6
votes
9
replies
929
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM Bowtie
updated 19 days ago by 39k • written 4 months ago by ▴ 40
6
votes
12
replies
1.2k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r biomarker
updated 10 weeks ago by 39k • written 4.3 years ago by ▴ 290
6
votes
11
replies
913
views
Calculate RPKM
RPKM
10 weeks ago by Chris ▴ 100
6
votes
7
replies
1.4k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters Algorithm Software
updated 18 days ago by 39k • written 6.0 years ago by ▴ 90
6
votes
7
replies
4.2k
views
8 follow
desktop bioinformatics platform specs
hardware desktop
updated 5 months ago by 39k • written 7.9 years ago by ▴ 610
6
votes
6
replies
3.0k
views
What does it mean for a snp to be enriched?
next-gen R SNP genome
updated 10 months ago by 39k • written 7.3 years ago by ▴ 40
1,000 results • Page 2 of 20
Recent Votes
Answer: How do you add an ORF that overlaps the two regions where a circular genome is c
C: PLINK logistic regression analysis and covariates
Comment: Regular Expression for conversion
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
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Recent Replies
Comment: Unusual FASTQ file by Ram 39k
People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more…
Comment: How to make a dotplot for bulk RNA average expression ? by bhumm ▴ 40
I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
Answer: What is the best way to clean bulk RNA-seq data? by swbarnes2 13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data? by Vincent Laufer ★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file by bhumm ▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline by ATpoint 72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline by swbarnes2 13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline by Ram 39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline by turcoa1 • 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline by Ram 39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline by turcoa1 • 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree by GenoMax 129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline by Ram 39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index by ashleymb1116 • 0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index by GenoMax 129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
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