Limit : this year
all time today this week this month this year
1,000 results • Page 1 of 20
Sort: Votes
Rank Views Votes Replies
23
votes
22
replies
36k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink vcf fam gatk vcftools
updated 9 weeks ago by • 0 • written 4.7 years ago by ▴ 250
19
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 6 months ago by 37k • written 7.1 years ago by ▴ 180
18
votes
19
replies
1.5k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq sequencing igv alignment next-gen
updated 9 weeks ago by 37k • written 4.1 years ago by • 0
18
votes
7
replies
742
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2 Variable RNA-seq
4 months ago by Rafael Soler ★ 1.1k
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 9 months ago by 37k • written 8.0 years ago by ▴ 920
14
votes
5
replies
2.6k
views
bioinformatics basic training
genome Tutorial
updated 11 months ago by 37k • written 8.2 years ago by • 0
12
votes
8
replies
542
views
Align 16S sequence to a reference
16S sequence alignment
updated 4 months ago by 2.9k • written 4 months ago by ▴ 120
12
votes
13
replies
2.1k
views
Gene Expression and Systems Biology (homework)
gene homework
updated 8 weeks ago by 37k • written 7.6 years ago by • 0
11
votes
9
replies
2.0k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash samtools awk
updated 6 weeks ago by 37k • written 7.6 years ago by ★ 2.5k
10
votes
2
replies
332
views
any script that can do this task
shell-script
updated 10 months ago by 37k • written 10 months ago by ▴ 10
10
votes
5
replies
6.1k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing Assembly alignment
updated 5 months ago by 37k • written 7.4 years ago by ★ 1.7k
10
votes
11
replies
8.1k
views
How to adjust my manhattan plot to look better?
qqman manhattan R
updated 8 months ago by 37k • written 7.9 years ago by ▴ 40
10
votes
8
replies
1.8k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 7 months ago by 37k • written 7.8 years ago by ▴ 30
9
votes
2
replies
338
views
Answer needed urgently
Deep
updated 4 months ago by ★ 22k • written 4 months ago by • 0
9
votes
9
replies
1.2k
views
Which hg38 file?
reference hg38 NCBI
updated 5 months ago by ▴ 80 • written 6 months ago by ▴ 50
9
votes
1
reply
5.3k
views
Why does MACS2 report multiple records for the same peak region?
ChIP-Seq macs macs2
updated 5 months ago by 37k • written 7.3 years ago by ★ 3.4k
9
votes
7
replies
719
views
Reference genome location
reference positions FASTA alignment genome
updated 29 days ago by ★ 1.2k • written 4 weeks ago by • 0
9
votes
7
replies
650
views
ChIP-seq; investigate binding within region of tRNA genes
tRNA ChIP nf-core ChIP-seq
updated 8 months ago by 37k • written 9 months ago by ▴ 20
9
votes
4
replies
1.9k
views
[Code] Converte fasta/fa files to fastq
perl fastq sed fasta
updated 5 months ago by 37k • written 7.2 years ago by ★ 9.2k
9
votes
4
replies
5.2k
views
How to analyse normalized read count?
RNA-Seq R
updated 4 weeks ago by 37k • written 7.7 years ago by ▴ 150
9
votes
14
replies
3.6k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 10 months ago by 37k • written 8.0 years ago by ▴ 70
9
votes
1
reply
3.2k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq qc
updated 5 months ago by 37k • written 7.7 years ago by ★ 2.6k
9
votes
4
replies
340
views
RNA seq, secreted protein
protein gene secreted
updated 7 weeks ago by 20k • written 8 weeks ago by ▴ 160
8
votes
11
replies
1.1k
views
using STAR instead of HISAT2
STAR
updated 6 months ago by 37k • written 6 months ago by ▴ 60
8
votes
3
replies
4.9k
views
Bioinformatics project for a beginner
projects
updated 6 months ago by 37k • written 7.1 years ago by ▴ 30
8
votes
5
replies
11k
views
samtools tview symbols
samtools
updated 3 months ago by 37k • written 7.5 years ago by ★ 1.4k
8
votes
4
replies
1.7k
views
using different tools to identify differential exprssed genes
rna-seq RNA-Seq R
updated 4 months ago by 37k • written 7.4 years ago by ▴ 20
8
votes
9
replies
2.0k
views
6 follow
Big difference in estimated duplicate reads between forward and reverse of paired-end RNA-seq
RNA-Seq duplication fastqc
updated 7 months ago by ▴ 690 • written 3.2 years ago by ★ 2.0k
8
votes
20
replies
1.7k
views
Converting runpsipred Script to Work on Windows OS
psipred windows
updated 8 months ago by 37k • written 4.5 years ago by ▴ 270
8
votes
3
replies
438
views
Package installation error using Bioconda
antismash Bioconda
8 weeks ago by A_heath ▴ 120
8
votes
9
replies
2.6k
views
error in rstudio
csv matrix rstudio
updated 4 months ago by 37k • written 7.5 years ago by ★ 4.1k
8
votes
5
replies
3.0k
views
Is it possible to guess sequencing platform used based on a FASTQ/BAM file?
BAM FASTQ
updated 6 weeks ago by 37k • written 7.6 years ago by ▴ 60
8
votes
6
replies
688
views
How to apply bioinformatic in vaccine design?
Vaccine
updated 11 weeks ago by ★ 2.2k • written 11 weeks ago by ▴ 30
7
votes
7
replies
1.0k
views
LRT test with DESeq2 and how to interpret the results
significant LRT DESeq2 genes RNA-Seq
updated 6 months ago by ★ 1.1k • written 8 months ago by ▴ 20
7
votes
8
replies
1.6k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock gene-duplication phylogeny
updated 11 hours ago by 37k • written 7.7 years ago by ▴ 20
7
votes
10
replies
3.3k
views
Choosing phylogenetic approaches
phylogeny
updated 11 months ago by 37k • written 8.4 years ago by ▴ 100
7
votes
4
replies
3.2k
views
Abra for indel realignment
realignment abra gatk
updated 11 months ago by 37k • written 8.2 years ago by ▴ 620
7
votes
8
replies
3.3k
views
remove duplicated entries from BLAST result file
blast alignment
updated 6 weeks ago by 37k • written 7.7 years ago by ▴ 150
7
votes
6
replies
2.1k
views
Optical duplicates?
duplicate optical
updated 11 months ago by ▴ 60 • written 20 months ago by ★ 1.2k
7
votes
4
replies
1.3k
views
microarray gene datasets
gene
updated 14 hours ago by 37k • written 7.7 years ago by ▴ 60
7
votes
5
replies
3.6k
views
Trinity de novo transcript assembly too many transcripts
RNA-Seq Assembly
updated 6 months ago by 37k • written 7.6 years ago by ▴ 780
7
votes
10
replies
3.7k
views
PSMC using haploid genomes
haploid genome PSMC
updated 11 months ago by 37k • written 8.2 years ago by ▴ 200
7
votes
13
replies
3.6k
views
DESeq2: can I correct for relatedness when using data from multiplex families?
DESeq2 RNA-Seq Multiplex-families
updated 9 months ago by 37k • written 8.0 years ago by ▴ 580
7
votes
4
replies
927
views
Are there mm39/GRCm39 blacklist regions?
blacklist
8 months ago by Ian 5.9k
7
votes
2
replies
3.1k
views
Counting reads for gene transcripts with overlapping loci
RNA-Seq gene R
updated 29 days ago by 37k • written 7.7 years ago by ▴ 70
7
votes
4
replies
4.0k
views
IGV genome browser problems
igv
updated 8 weeks ago by 37k • written 7.6 years ago by ▴ 210
7
votes
9
replies
700
views
Tools to check the length of isoforms in reference transcript
transcript histogram isoform
3 months ago by Jjbox ▴ 30
7
votes
6
replies
1.1k
views
Perseus like missing value replacement in Python
Python free Data LFQ-intensities proteomics analysis Lable
11 months ago by Balasubramaniam ▴ 20
7
votes
4
replies
2.0k
views
RSEM BAM outputs, which one to use for RSeQC?
RSEM STAR RSeQC BAM
10 months ago by Freek ▴ 50
7
votes
7
replies
918
views
GSEA analysis
Hi
updated 9 months ago by ▴ 10 • written 9 months ago by ▴ 10
1,000 results • Page 1 of 20
Recent Votes
Answer: 'SyntaxError': 'return' outside function?
Comment: Analyzing bulk RNA-seq
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: IGV coverage bar has color, but no mutation?
Answer: What is the difference between a Read and a Fragment in RNA-seq?
lncRNA analysis tutorial
Answer: 2D structure of a custom protein (not in any databases) from a PDB file.
Recent Locations • All
Germany, 1 minute ago
India, 3 minutes ago
Pakistan, 3 minutes ago
France, 5 minutes ago
United Kingdom, 6 minutes ago
Spain, 7 minutes ago
India, 7 minutes ago
Recent Awards • All
Teacher to natasha.sernova ★ 3.9k
Popular Question to Genotepes ▴ 950
Scholar to schlogl ▴ 120
Scholar to vkkodali_ncbi ★ 3.4k
Commentator to i.sudbery 16k
Popular Question to amy__ ▴ 50
Scholar to Michael Dondrup 52k
Recent Replies
Comment: How to extract the list of genes from TCGA CNV data by Kevin Blighe 84k
Unfortunately it seems that *gaia* has been deprecated. You could still try to install a previous version of it, or set up a new conda envi…
Comment: RNASeq differential expression masked by pathways disregulation by ATpoint 68k
If this is the case then you cannot correct for anything as this effect is nested with center.
Comment: HTSeq error processing GFF file by barslmn ★ 1.2k
That error message is very descriptive. Could you also add the line 997531?
Comment: RNASeq differential expression masked by pathways disregulation by Gama313 ▴ 110
Thanks for the answer. However I am not sure this could be considered batch since CC2 samples have true upregulation of specific pathways t…
Comment: Is the heterozygosity flag (--het) in vcftools calculate observed and expected h by dr.fakharunnisa • 0
Hello #gubrins Have you found the answer
Comment: CoveragePlot in Signac from MACS2 Object by seidel 10k
The `object` will the the Seurat object you're working with, because that contains the data that will be plotted (Tn5 insertion events per …
Answer: Using Entrez Utilities to query the Nucleotide database by collection_date by GenoMax 125k
Using [**Entrezdirect**][1]. Date in last column is collection date. No way to query using it though. Could be wrong. $ esearch -db nu…
Comment: Faking hh-suite workflow / alignment output by Mensur Dlakic ★ 22k
Pretty sure that nothing other than HHsuite outputs results in `.hhr` format.
Answer: Manual Polygenic Risk Score calculation by Sam ★ 4.6k
Same allele = weight of 1, different allele = weight of 0. You can read more here: https://choishingwan.github.io/PRS-Tutorial/plink/#gener…
Comment: Single sample GSEA analysis by tujuchuanli ▴ 100
Hi jv, Thank you for your help. But I am still uncertain. The GSEA tools can process the preranked list. However, it still required that I…
Answer: 2D structure of a custom protein (not in any databases) from a PDB file. by Jiyao Wang ▴ 290
You can also try out [iCn3D](https://structure.ncbi.nlm.nih.gov/icn3d). After you load your custom PDB via the menu "File > Open File > PDB…
Comment: CoveragePlot in Signac from MACS2 Object by bioinformatics.girl • 0
What is 'peaks' entered as?... The input is: CoveragePlot( object = pbmc, region = "CD8A", ranges = peaks, …
Comment: Faking hh-suite workflow / alignment output by Nick ▴ 40
I totally get your point, maybe long-winded was also not the right description for my issue. One example, [custom databases][1] are very cl…
Comment: CoveragePlot in Signac from MACS2 Object by seidel 10k
Wouldn't you take your MACS2 files, import them with rtracklayer so that they are GRanges objects, and then pass those as the peaks? i.e. w…
Comment: RNAseq for DE purpose by swbarnes2 13k
Honestly, I think most RNASeq aligners are fairly robust to adapters. You could probably get away with not trimming at all
Traffic: 2057 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6