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1,000 results • Page 2 of 20
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7
votes
6
replies
851
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 4 months ago by 76k • written 4 months ago by ▴ 180
7
votes
5
replies
2.3k
views
using machine learning regards to ribo-seq data sets
gene-regulatory-network ribo-seq machine-learning
updated 11 months ago by 40k • written 8.1 years ago by ★ 4.2k
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
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
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
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
588
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
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
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
3
replies
1.8k
views
PLINK results interpretation
SNP software-error
updated 12 months ago by 40k • written 8.2 years ago by ▴ 40
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
543
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
2.8k
views
ChIP-Seq Intensity Analysis
R ChIP-Seq
updated 4 months ago by 40k • written 5.8 years ago by ▴ 20
6
votes
2
replies
667
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
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
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
13
replies
1.1k
views
Error with STAR
STAR
updated 6 months ago by 40k • written 6 months ago by ▴ 180
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
4
replies
518
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
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
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
2
replies
561
views
Need to Modify this
language R
updated 9 months ago by 76k • written 9 months ago by • 0
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
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
4
replies
578
views
Equivalent to SeqMan alignment tool
SeqMan alignments
7 months ago by A_heath ▴ 140
6
votes
7
replies
4.6k
views
Creation Of A .Bed File From .Txt
plink
updated 6 months ago by 40k • written 9.6 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
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
11
replies
1.2k
views
Calculate RPKM
RPKM
6 months ago by Chris ▴ 180
6
votes
3
replies
310
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
966
views
Help with error in cellranger
Cellranger
updated 4 months ago by 134k • written 4 months ago by ▴ 180
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
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
1
reply
282
views
16S vs shotgun tools
metagenomics
8 weeks ago by anasjamshed ▴ 120
5
votes
9
replies
2.6k
views
differential expression analysis tools for single end reads
rna-seq next-gen
updated 11 months ago by 40k • written 8.1 years ago by ▴ 90
5
votes
3
replies
560
views
GENE code ID conversion
ensembl entrez
5 months ago by Confused_human ▴ 10
5
votes
14
replies
3.1k
views
How to Calulate Allele Frequency from a VCF File?
frequency allele VCF
updated 7 months ago by 21k • written 8 months ago by • 0
5
votes
5
replies
573
views
gvcf to bam or fastq
fastq NGS bam gvcf
11 months ago by OMG_HG • 0
5
votes
4
replies
1.8k
views
MyVariant.info fields descriptions?
genome snp variant
updated 6 months ago by 40k • written 7.4 years ago by ▴ 90
5
votes
6
replies
693
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
1,000 results • Page 2 of 20
Recent Votes
How to assign read groups to bam files?
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Answer: Which function is best for pathway analysis?
Comment: Hisat2 index and alignment question
Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
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Recent Replies
Answer: Fetch Fastq files directly for SRA data by Rob 6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe by YUYANG.OON • 0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis? by Chris ▴ 180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject by Qi • 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis? by Yogi ▴ 20
Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions by Yogi ▴ 20
Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question by Istvan Albert 98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate by dsull ★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
Comment: Troubles launch IGV on Linux(Debian) by morovatunc ▴ 550
Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
Comment: How to check RNAseq support for annotated genes? by Michael 53k
> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate by Mehwish • 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
Comment: Violin plot (Monocle 3) - Troubleshooting by Ram 40k
The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…
Comment: Violin plot (Monocle 3) - Troubleshooting by bk11 ★ 1.2k
I m not sure why you have problem there. I do not encounter any problem. May be your gene list are not present in your source object. Pleas…
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