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1,000 results • Page 4 of 20
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6
votes
13
replies
657
views
Error with STAR
STAR
updated 22 days ago by 38k • written 25 days ago by ▴ 70
4
votes
12
replies
382
views
Can I use abundance from Tximport to compare the expression level of transcript in same condition?
Salmon Tximport
updated 9 days ago by 38k • written 10 days ago by ▴ 20
6
votes
12
replies
12k
views
11 follow
Forum: Online/remote/distance learning/ - partime/fulltime - PhD, Bioinformatics in USA
PhD university
updated 22 days ago by 38k • written 6.5 years ago by ▴ 20
4
votes
12
replies
2.9k
views
Data retrieval from GEO
Microarray GEO
updated 8 days ago by 38k • written 5.6 years ago by ★ 1.3k
1
vote
12
replies
2.3k
views
GATK Mutect2 tumor mode
gatk mutect2 tumor human wgs
updated 28 days ago by • 0 • written 2.6 years ago by ▴ 230
4
votes
12
replies
1.2k
views
What is the command to download GTF from NCBI
ncbi gtf linux
updated 10 days ago by 38k • written 9 months ago by ▴ 10
6
votes
12
replies
1.1k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r biomarker
updated 14 days ago by 38k • written 4.2 years ago by ▴ 290
4
votes
12
replies
2.4k
views
Accessing MeDUSA methyl-seq download
MeDUSA methyl-seq
updated 7 days ago by 38k • written 8.2 years ago by ▴ 350
4
votes
12
replies
8.0k
views
how is obtained the BED score values (the 5th column of the bed files) in BED files
ChIP-Seq BED
updated 9 days ago by 38k • written 6.2 years ago by ▴ 250
4
votes
12
replies
1.2k
views
vg augment/call - Excessively high memory usage for some chromosomes
vg-toolkit vg-augment vg vg-call vgteam
16 days ago by Andrew ▴ 20
3
votes
12
replies
558
views
prefix extraction and preparation for mapping and variant calling
bash
updated 9 days ago by 20k • written 15 days ago by • 0
6
votes
12
replies
7.3k
views
7 follow
Problem When Downloading Large Number Of Sequences From Genbank
genbank
updated 8 days ago by 38k • written 10.9 years ago by ▴ 290
2
votes
12
replies
14k
views
How to download list of compounds from pubchem database using command line
software-error alignment
updated 14 days ago by 38k • written 6.8 years ago by ▴ 10
7
votes
12
replies
3.5k
views
How to filter transcripts with overlapping exons?
bed RNA-Seq
updated 9 days ago by 38k • written 8.4 years ago by ▴ 390
20
votes
12
replies
4.5k
views
7 follow
Simple Fasta Parsing Is Not Simple.
fasta python biopython
updated 8 days ago by 38k • written 12.9 years ago by ▴ 120
8
votes
12
replies
8.4k
views
7 follow
How to make sure there is no duplicate sequence in a fasta file?
fasta sequence
updated 9 days ago by 38k • written 7.5 years ago by ★ 1.8k
2
votes
12
replies
564
views
how to get to a VCF from bam files
Mpileup Samtools BAM bcftools VCF
updated 7 days ago by 38k • written 9 days ago by • 0
2
votes
12
replies
952
views
EC file parsing
bash shell
updated 9 days ago by 38k • written 5.4 years ago by ▴ 110
8
votes
12
replies
2.5k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 14 days ago by 38k • written 19 months ago by ▴ 30
6
votes
12
replies
749
views
6 follow
gtf2bed not converting to bed
bed gtf
updated 13 days ago by 7.8k • written 16 days ago by ▴ 60
21
votes
12
replies
9.8k
views
7 follow
An Alternative To Rsync (Or Useful Parameters)
next-gen-sequencing
updated 4 days ago by 38k • written 11.5 years ago by 4.3k
6
votes
12
replies
1.2k
views
VCF files 101 - for people from non Bioinformatics Background
vcf sequencing genome variant-calling
updated 18 days ago by 38k • written 2.6 years ago by ▴ 20
0
votes
12
replies
1.5k
views
bedtools intersect issue
bed bedtools
updated 9 days ago by 38k • written 4.6 years ago by ▴ 120
9
votes
12
replies
28k
views
6 follow
How To Download Gene Sequences From Ncbi Gene
ncbi fasta gene
updated 7 days ago by 38k • written 11.3 years ago by ▴ 20
2
votes
12
replies
871
views
Generating vcf files per individual instead of one big file from bam files
vcf bam variant
updated 10 days ago by 38k • written 7 months ago by ▴ 70
0
votes
12
replies
2.2k
views
How to download large protein data from NCBI?
protein NCBI
updated 7 days ago by 38k • written 4.8 years ago by ▴ 30
6
votes
12
replies
2.9k
views
Forum: Google Summer Of Code 2014 Gsoc 2014
GSOC
updated 28 days ago by 38k • written 9.1 years ago by ★ 1.2k
8
votes
11
replies
1.2k
views
6 follow
Forum: Paper: Ten simple rules for biologists initiating a collaboration with computer scientists
article opinion
updated 22 days ago by 38k • written 2.4 years ago by 13k
6
votes
11
replies
786
views
Calculate RPKM
RPKM
11 days ago by Chris ▴ 70
2
votes
11
replies
993
views
gseKEGG - no gene can be mapped (RNAseq analysis)
RNAseq cluster-profiler KEGG GSEA
28 days ago by redafazazi ▴ 20
6
votes
11
replies
783
views
Blog: How to choose Normalization methods (TPM/RPKM/FPKM) for mRNA expression
mRNA-seq gene-expression normalization-methods TPM
updated 27 days ago by 16k • written 4 weeks ago by ▴ 240
11
votes
11
replies
1.4k
views
read.table function loss of columns in bed file
R
updated 14 days ago by 38k • written 6.0 years ago by • 0
11
votes
11
replies
10.0k
views
Convert fastq.gz to fastq.bgz
NGS FASTQ
updated 14 days ago by 38k • written 5.2 years ago by ▴ 20
3
votes
11
replies
2.0k
views
Detecting error in Ubuntu environment
fasta Ubuntu
updated 9 days ago by 38k • written 5.1 years ago by ▴ 20
11
votes
11
replies
3.0k
views
8 follow
Forum: Best open source genome browser in 2020
genome-browser genomics
updated 10 days ago by 38k • written 2.4 years ago by ▴ 30
6
votes
11
replies
1.5k
views
7 follow
How do I interpret a 200bp reduction of coverage in a gene exon?
read-depth coverage golden-helix bam
updated 9 days ago by 38k • written 23 months ago by • 0
10
votes
11
replies
9.1k
views
Where Is Mirna Binding Site On Mrna ?
mRNA transcript miRNA
updated 29 days ago by 38k • written 9.2 years ago by ▴ 500
4
votes
11
replies
457
views
Align miRNA library (small RNA-seq) without trimming
BOWTIE2 RNA-SEQ BOWTIE
1 day ago by Paola ▴ 10
1
vote
11
replies
1.6k
views
Extract information from gtf file
GTF
updated 14 days ago by 38k • written 13 months ago by • 0
10
votes
11
replies
3.2k
views
Forum: 48 Replicate RNA-Seq Study Points to Replicates Needed for DGE
RNA-seq differential-gene-expression
updated 10 days ago by 38k • written 7.9 years ago by ▴ 640
4
votes
11
replies
1.6k
views
Use BLAST Command Line Applications on combined FASTA files
BLAST
updated 14 days ago by 38k • written 18 months ago by ▴ 30
0
votes
11
replies
2.6k
views
Affymetrix Power Tools Error
software-error CEL APT Microarray gene
updated 9 days ago by 38k • written 6.6 years ago by ▴ 10
40
votes
11
replies
6.4k
views
9 follow
Forum: "An Explosion Of Bioinformatics Careers" - from Science Careers
career
updated 25 days ago by 38k • written 8.8 years ago by 3.2k
2
votes
11
replies
9.2k
views
9 follow
CD-HIT Clustering output
Clustering CD-HIT
updated 3 days ago by ▴ 10 • written 8.7 years ago by • 0
19
votes
11
replies
18k
views
How to transpose large amounts of datasets in excel
Transpose excel
updated 7 days ago by 38k • written 7.7 years ago by ▴ 30
16
votes
11
replies
1.2k
views
10 follow
Forum: Suggest common programming tasks for biologists who are novice programmers
education
updated 22 days ago by 38k • written 2.1 years ago by ▴ 40
0
votes
11
replies
900
views
filtering multi sample vcf file
vcf
updated 10 days ago by 38k • written 7 months ago by • 0
3
votes
11
replies
2.3k
views
mm9 RNA-seq reference genome
alignment sequencing RNA-seq gene
updated 17 days ago by 38k • written 4.6 years ago by ▴ 120
7
votes
11
replies
1.4k
views
6 follow
how to convert to computational biology from bioinformatics
software computational-biology algorithm
updated 14 days ago by 38k • written 21 months ago by • 0
16
votes
11
replies
13k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 17 days ago by 38k • written 6.4 years ago by ★ 4.6k
1,000 results • Page 4 of 20
Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Recent Replies
Comment: SKAT in R by Eliza ▴ 20
@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
Comment: TCGA-BRCA tissue and RNAseq problem by pinheirofabiano ▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic by antoine.fauchois92 • 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values by Eliza ▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids? by GenoMax 127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL by rpolicastro 11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created by DdogBoss • 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate by ATpoint 71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate by Ram 38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis by rpolicastro 11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files by Darrenjdd • 0
Perfect! Thank you!
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