Limit : this year
all time today this week this month this year
1,000 results • Page 1 of 20
Sort: replies
Rank Views Votes Replies
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
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
5
votes
22
replies
6.3k
views
SVM for classified gene expression data
R svm microarray
updated 6 months ago by 37k • written 7.1 years ago by ▴ 50
2
votes
22
replies
1.0k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree linkage genetics
3 months ago by Joel Wallenius ▴ 100
0
votes
21
replies
1.4k
views
HTSeq-Count: no_feature too high?
htseq-count
3 months ago by sea.joson ▴ 10
5
votes
20
replies
3.1k
views
DiscoSnp Segmentation fault
snp discosnp
updated 4 months ago by 37k • written 7.4 years ago by ▴ 130
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
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
0
votes
19
replies
963
views
scatterplot in R
microarray expression gene
updated 4 months ago by 37k • written 4 months ago by ▴ 10
7
votes
19
replies
2.3k
views
mapping script process sleeping on server.
alignment
updated 8 months ago by 37k • written 7.9 years ago by ▴ 30
2
votes
18
replies
1.6k
views
I need help in this
gene weblems alignment
updated 6 months ago by 37k • written 7.1 years ago by • 0
3
votes
18
replies
785
views
6 follow
What sequencing/alignment artifact is this?
variants mutect sequencing alignment mitochondria
3 months ago by lacb ▴ 30
4
votes
18
replies
3.2k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq virus reads fusion
updated 5 months ago by 37k • written 7.2 years ago by ▴ 60
7
votes
18
replies
7.5k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 11 months ago by 37k • written 8.2 years ago by ▴ 190
0
votes
17
replies
4.0k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 4 months ago by 37k • written 7.4 years ago by ▴ 30
0
votes
17
replies
5.4k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping genome fastq STAR
updated 11 months ago by • 0 • written 2.1 years ago by • 0
0
votes
16
replies
3.5k
views
Count read with summarizeOverlaps result 0 for all sample
RNA-Seq
updated 7 months ago by 37k • written 7.8 years ago by ▴ 550
0
votes
16
replies
1.2k
views
How to convert ncbi gff file to ensembl gff format
file gff
5 months ago by yoser4 ▴ 10
4
votes
16
replies
926
views
How to extract intron counts from total RNA Sequencing?
featurecounts RNAseq htseq STAR
11 weeks ago by barrypraveen ▴ 100
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
3
votes
15
replies
1.1k
views
Overlapping regions in a BED file
regions BED Sequence exons annotation
7 months ago by Matej • 0
6
votes
15
replies
891
views
The Best Cloud Solution For Genomics
cloud data-sharing genomics workflow
updated 6 months ago by 37k • written 7 months ago by ▴ 50
0
votes
15
replies
1.3k
views
Chromosome accession numbers correspond to which chromosome?
bam chromosome bed
3 months ago by amy__ ▴ 50
7
votes
15
replies
4.4k
views
6 follow
blastn error - NCBI C++ Exception
assembly blast alignment
updated 10 months ago by 14k • written 22 months ago by ▴ 970
0
votes
15
replies
2.9k
views
Identify genes in a tophat aligned bam/sam file
blast alignment rna-seq gene
updated 5 weeks ago by 37k • written 7.6 years ago by • 0
0
votes
14
replies
972
views
Corrplot heatmap crunched up and unreadable
Corrplot heatmap
8 months ago by aropri ▴ 110
2
votes
14
replies
682
views
Annotating the multi sample vcf file
vcf annotation
7 weeks ago by Peerzada • 0
0
votes
14
replies
831
views
Error using HTSEq_count
HTSeq python
17 days ago by felipead66 ▴ 110
5
votes
14
replies
1.3k
views
Removing sequences that contain deletion mutations in them from a fasta file (with python)
python
6 months ago by Mustafa ▴ 10
5
votes
14
replies
633
views
How to Calulate Allele Frequency from a VCF File?
frequency allele VCF
updated 2 days ago by 21k • written 6 days ago by • 0
5
votes
14
replies
1.2k
views
Fastqc genome reads
genome fastqc
updated 11 months ago by 68k • written 11 months ago by ▴ 60
1
vote
14
replies
1.4k
views
Counts all read zero after alignment?
alignment rna-seq
updated 7 months ago by 37k • written 17 months ago by • 0
6
votes
14
replies
2.5k
views
mapping RNAseq reads to a genbank isoforme that is not in Reference Annotation
RNA-Seq sequence cufflinks new isoform in rnaseq
updated 6 months ago by 37k • written 7.0 years ago by • 0
0
votes
14
replies
3.1k
views
ABySS - Out of memory using 64 cores (520GB)
abyss assembly
updated 3 months ago by 37k • written 7.5 years ago by • 0
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
5
votes
13
replies
5.9k
views
makeblastdb problem for bacterial genomes
blast makeblastdb
updated 12 months ago by 37k • written 8.2 years ago by ▴ 90
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
2
votes
13
replies
912
views
How to compare differential expression of same genes between two groups?
expression differential
updated 10 months ago by 13k • written 10 months ago by ▴ 20
1
vote
13
replies
2.3k
views
If GI number in list1 is present in genbank file, make new list and append location information
python genbank biopython
updated 9 months ago by 37k • written 7.9 years ago by ▴ 80
6
votes
13
replies
5.9k
views
DESeq2 and edgeR - no agreement between results
RNA-Seq edgeR DESeq2
updated 5 months ago by 37k • written 7.2 years ago by ▴ 60
2
votes
13
replies
1.2k
views
[RNAseq, featureCounts] Can paired-end data be processed as single end?
paired-end RNAseq featureCounts
5 months ago by Texx • 0
1
vote
13
replies
810
views
Samtools indexing problem during bwa mem alignment
Alignment bwa samtools
7 months ago by GlouGlou • 0
1
vote
13
replies
3.2k
views
Clarification on the “orientation” of chromosomal rearrangements in mate-pair or paired-end sequencing
sequencing alignment Assembly
updated 9 months ago by 37k • written 8.0 years ago by ▴ 380
1
vote
13
replies
888
views
Ete3 build - ValueError: Error parsing Phyml result
ete3 ete3toolkit ete phyml build
updated 3 months ago by 2.9k • written 3 months ago by ▴ 50
4
votes
13
replies
23k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 7 months ago by • 0 • written 4.9 years ago by ▴ 20
0
votes
13
replies
274
views
RNAseq for DE purpose
RNAseq
updated 11 hours ago by 13k • written 14 hours ago by • 0
1
vote
13
replies
2.5k
views
Pooled / polyploid samples
discosnp
updated 4 months ago by 37k • written 7.4 years ago by ▴ 60
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
1
vote
12
replies
3.3k
views
why different outputs with applying various extracting fasta sequences tool, which one correct!?
alignment sequencing RNA-Seq
updated 3 months ago by 37k • written 7.5 years ago by ★ 1.7k
0
votes
12
replies
3.5k
views
Problem: kmergenie has a minimum number of input of reads?
K-mers Kmergenie
updated 9 months ago by 37k • written 7.9 years ago by ▴ 90
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
Hungary, just now
Germany, just now
France, 2 minutes ago
Prague, Czech republic, 3 minutes ago
Taiwan, 3 minutes ago
Germany, 6 minutes ago
Pakistan, 6 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: 2035 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