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921 results • Page 3 of 19
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6
votes
7
replies
2.5k
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getting a consense one header .fasta file from a genic region, from .bam template
fasta bam
updated 4 days ago by 38k • written 5.3 years ago by ▴ 80
6
votes
5
replies
5.1k
views
Ensembl Hg38 dna, dna_rm, and dna_sm
ensembl alignment sequencing
updated 4 days ago by ▴ 30 • written 7.9 years ago by ▴ 550
6
votes
12
replies
1.1k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r biomarker
updated 4 days ago by 38k • written 4.2 years ago by ▴ 290
6
votes
10
replies
2.5k
views
Genome assembly with RNA-seq data?
Assembly genome RNA-Seq
updated 15 hours ago by 38k • written 6.6 years ago by ★ 2.0k
6
votes
1
reply
1.7k
views
News: Are protein domains indivisible?
Athropy Domains Proteins
updated 11 hours ago by 38k • written 7.8 years ago by ★ 4.2k
6
votes
11
replies
682
views
Calculate RPKM
RPKM
1 day ago by Chris ▴ 70
6
votes
4
replies
769
views
Forum: What are the major advances in Bioinformatics since 2016
Bioinformatics
updated 5 days ago by 38k • written 20 months ago by ▴ 30
5
votes
5
replies
1.3k
views
Forum: Beginner: looking for suggestions
computer-science
updated 4 days ago by 38k • written 4.2 years ago by • 0
5
votes
4
replies
377
views
Languages for Bioinformatics
python biopython R
updated 5 days ago by 38k • written 11 days ago by • 0
5
votes
3
replies
363
views
News: March 13-16: Virtual Nextflow and nf-core training event in 5 languages
nf-core pipeline Nextflow
updated 1 day ago by ▴ 230 • written 4 weeks ago by 3.4k
5
votes
5
replies
4.8k
views
Which kind of microRNAs expression are measured in TCGA?
next-gen RNA-Seq genome tcga
updated 15 hours ago by 38k • written 8.8 years ago by ▴ 960
5
votes
3
replies
4.5k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 5 days ago by • 0 • written 5.4 years ago by ▴ 130
5
votes
4
replies
2.9k
views
BEDOPS closest features help
bed methylation bedops bedtools-closest
updated 4 days ago by 38k • written 7.3 years ago by ▴ 20
5
votes
4
replies
3.4k
views
primer3 parameter input
linux primer3 bacteria gene
updated 4 days ago by 38k • written 4.5 years ago by ▴ 20
5
votes
1
reply
651
views
Is there a programmatic way to extract the Gene Description of a gene given the Gene Symbol?
NCBI genes
updated 4 days ago by 38k • written 2.1 years ago by ▴ 10
5
votes
3
replies
631
views
Mapping chromosome location to gene ID
bedtools eclip ensembl bed R
updated 4 days ago by 38k • written 9 months ago by ▴ 30
5
votes
10
replies
1.7k
views
Is it possible to count lines of fastq.gz file in R ?
fastq R
updated 4 days ago by 38k • written 18 months ago by • 0
5
votes
2
replies
2.0k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 4 days ago by 38k • written 4.3 years ago by ▴ 50
5
votes
5
replies
751
views
rgb to hex in GRanges Object in R
ChIP-Seq R
updated 16 hours ago by 38k • written 2.4 years ago by ▴ 20
5
votes
19
replies
7.5k
views
How to generate contigs from bam alignment
bam Assembly contigs
updated 4 days ago by 38k • written 7.6 years ago by ▴ 10
5
votes
3
replies
3.6k
views
How convert files .psl to files .bed?
bed awk psl
updated 4 days ago by 38k • written 6.8 years ago by • 0
5
votes
4
replies
1.5k
views
Noob question: replacing ensembl ID with the gene symbol?
ensembl gse
updated 4 days ago by 38k • written 16 months ago by ▴ 10
5
votes
2
replies
3.2k
views
News: Summary of AGBT 2015
AGBT2015 AGBT
updated 5 days ago by 38k • written 8.1 years ago by ▴ 640
5
votes
6
replies
1.0k
views
Analyzing counts over 3 different timepoints and 2 conditions with DESeq2
deseq2
updated 4 days ago by 38k • written 16 months ago by ▴ 10
5
votes
3
replies
852
views
Can collection of work become a PHD thesis in Bioinformatics
thesis phd
updated 16 hours ago by 38k • written 2.3 years ago by ▴ 50
5
votes
3
replies
1.3k
views
News: Bioinfo-Core Conference Call, October 17, 2017 (11 am EDT USA, local times around world)
bioinfo-core
updated 16 hours ago by 38k • written 5.6 years ago by 127k
5
votes
11
replies
5.8k
views
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]
HuEx-1_0-st R
updated 1 day ago by 38k • written 5.0 years ago by ▴ 20
5
votes
5
replies
3.3k
views
Differential expression analysis tool for single cell RNA-seq data
single-cell RNA-seq DE analysis RNA-Seq
updated 4 days ago by ▴ 120 • written 5.4 years ago by ▴ 80
5
votes
9
replies
1.9k
views
Program to find genes up/down-regulated by a given gene
geo upregulated gene downregulated
updated 5 days ago by 38k • written 8.1 years ago by ▴ 500
4
votes
3
replies
267
views
How to implement this two-stage one-to-many workflow using WDL?
wdl
updated 1 hour ago by • 0 • written 1 day ago by ▴ 70
4
votes
2
replies
135
views
Forum: advice on course selection for a bioinformatics career.
career
updated 15 hours ago by 96k • written 15 hours ago by • 0
4
votes
13
replies
910
views
6 follow
select rows in a tab-delimited ed file
linux text
updated 12 hours ago by 38k • written 8 months ago by ▴ 40
4
votes
4
replies
258
views
Please give me a grep command to get Gene IDS and TPM values from a stringtie output gtf file
grep Stringtie awk RNA-seq gtf
6 days ago by sreelekha ▴ 10
4
votes
2
replies
7.9k
views
What is the best practice for BAM sorting?
RNA-Seq samtools STAR
updated 1 day ago by 38k • written 7.9 years ago by ▴ 350
4
votes
5
replies
450
views
colouring variables in r
R
updated 3 days ago by 11k • written 4 days ago by • 0
4
votes
10
replies
1.3k
views
bash script for merging R1 and R2 reads
fastq bash illumina
updated 4 days ago by 38k • written 9 months ago by ▴ 10
4
votes
6
replies
8.7k
views
Does bowtie2 take gz input files?
fastq gzip bowtie2
updated 4 days ago by 38k • written 3.4 years ago by • 0
4
votes
2
replies
981
views
Large table reformatting
vcf linux
updated 4 days ago by 38k • written 5.4 years ago by ▴ 20
4
votes
2
replies
255
views
Book for RNASeq analysis recommendation
RNAseq_analysis book ebook recommendations
updated 4 days ago by 96k • written 5 days ago by ▴ 30
4
votes
2
replies
244
views
align reads to a custom reference genome
reference_genome custom
updated 4 days ago by 4.5k • written 4 days ago by • 0
4
votes
2
replies
433
views
bioinformatic cost of whole genome sequencing
WGS Whole-Genome-Sequencing NGS
updated 16 hours ago by 38k • written 8 months ago by ▴ 10
4
votes
11
replies
1.6k
views
Use BLAST Command Line Applications on combined FASTA files
BLAST
updated 4 days ago by 38k • written 18 months ago by ▴ 30
4
votes
12
replies
669
views
6 follow
gtf2bed not converting to bed
bed gtf
updated 2 days ago by 7.7k • written 6 days ago by ▴ 60
4
votes
8
replies
1.6k
views
visualize my .BAM file in IGV
RNA bowtie2 IGV alignment BAM
updated 4 days ago by 38k • written 2.9 years ago by ▴ 20
4
votes
7
replies
2.4k
views
How can I deepen my knowledge in NGS data analysis?
ngs gene
updated 14 hours ago by 38k • written 5.9 years ago by • 0
4
votes
2
replies
291
views
bedtools
bed bam bedtools
updated 4 days ago by 38k • written 7 months ago by • 0
4
votes
5
replies
1.6k
views
How to apply for bioinformatics jobs
career
updated 1 day ago by 38k • written 8.0 years ago by • 0
4
votes
12
replies
1.1k
views
What is the command to download GTF from NCBI
ncbi gtf linux
updated 12 hours ago by 38k • written 8 months ago by ▴ 10
4
votes
2
replies
374
views
how to duplicate a column in different files with bash
bash
updated 3 days ago by ▴ 60 • written 6 months ago by ▴ 40
4
votes
8
replies
2.3k
views
7 follow
Converting an output de-novo transcriptome assembled with Trinity to a .gff3 file
Trinity
updated 1 day ago by 7.7k • written 3.5 years ago by ▴ 80
921 results • Page 3 of 19
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Gene Set Enrichment Analysis
Can I sort my bam files with Picard MergeSamFiles?
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
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Recent Replies
Comment: Can someone help me with searching overlapping values between two files? by mxm189 • 0
I tried some stuff but it didnt work. I used ChatGPT, because I'm not good at this. I tried sorting of the two files first # Sort the inp…
Comment: Survival analysis with gene expression by krushnach80 ★ 1.1k
Hello @kevinblighe I would like to get your help in [this][1] [1]: https://www.biostars.org/p/9558148/
Comment: activity of unloaded/unassembled Tn5 by callumjcparr • 0
![enter image description here][1] ![enter image description here][2] ![enter image description here][3] ![enter image description he…
Answer: How to implement this two-stage one-to-many workflow using WDL? by Ruben • 0
> Unfortunately, as far as I can tell, WDL provides no support for iterating over the contents of a directory. (I find this shocking. I con…
Answer: activity of unloaded/unassembled Tn5 by callumjcparr • 0
So I hope someone is still interested in this. We have taken to preparing recombinant Tn5 now as it's much cheaper than commercial suppli…
Comment: RNA-SEQ by ali • 0
thanks for your helping
Comment: TSS of protein coding genes by ConvolutedGenome ▴ 10
I am quite confused with GENCODE GTF file, So, within the GENCODE GTF file, I noticed that each (protein-coding) gene has multiple "transc…
Comment: Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq da by iraun 5.8k
Hi! I personally use [SplAdder][1], in case you want to add it to your list :). [1]: https://github.com/ratschlab/spladder
Answer: Problem generating a .vcf after upgrade of samtools and bcftools by Andy • 0
Really the only needed, that help worked, thank's
Comment: Active enhancers for mm39 by seidel 11k
Just curious what you mean by "active" enhancers. Enhancers are active in a given context (e.g. cell type developmental state, etc.), and m…
Comment: Creating loop for read groups using Picard by ntsopoul ▴ 20
try absolute paths navigate to the directory with cd and use pwd to get the absolute directory.
Comment: how to create interacting Hi-C peaks by rheab1230 ▴ 140
Thank you. I will use this package since I am more familiar with R
Comment: how to create interacting Hi-C peaks by rheab1230 ▴ 140
thank you. i will go through it
Comment: Fastqc report analysis by npavliukovec • 0
Yeah, after trimming and fastqc I will have to generate MultiQC plots and after do mapping with reference genome. As I know, for eukaryotes…
Comment: My fastq files(paired end) have different read number by kimgeng • 0
Oh, I see, Thank you however, I want to make vcf files with gatk haplotypecaller and GenotypeGVCFs. But I got some problems I have about 2.…
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