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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
0
votes
18
replies
1.9k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 9 months ago by
GenoMax
142k • written 9 months ago by
Apex92
▴ 280
1
vote
18
replies
2.7k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
7.8 years ago by
Tom
▴ 40
2
votes
18
replies
1.7k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
7 weeks ago by
b.contreras.moreira
▴ 200
3
votes
18
replies
3.3k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 2.8 years ago by
Ram
43k • written 2.9 years ago by
Nai
▴ 50
16
votes
18
replies
5.6k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.7 years ago by
Mensur Dlakic
★ 27k • written 4.7 years ago by
tikshyadav19
• 0
2
votes
18
replies
2.8k
views
Bwa on multiple processor
np
mpirun
bwa
alignment
2.4 years ago by
shivangi.agarwal800
▴ 120
14
votes
18
replies
2.4k
views
Clustering in single cell
seurat
single-cell
updated 7 months ago by
e.r.zakiev
▴ 210 • written 7 months ago by
Chris
▴ 280
4
votes
18
replies
4.2k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 21 months ago by
Ram
43k • written 8.5 years ago by
Joel TM
▴ 60
14
votes
18
replies
5.0k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 7.4 years ago by
Biostar
20 • written 7.6 years ago by
plink_9857
▴ 50
20
votes
17
replies
6.1k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
6.8 years ago by
Anand Rao
▴ 630
7
votes
17
replies
4.3k
views
Strange MA-plot using DESeq2
rna-seq
R
deseq2
updated 7.3 years ago by
Biostar
20 • written 7.5 years ago by
stan
▴ 80
16
votes
17
replies
3.2k
views
6 follow
RNA seq pipeline
RNA-Seq
6.6 years ago by
dimitrischat
▴ 210
0
votes
17
replies
3.7k
views
WGCNA error: "Error in cutreeDynamic"
rna-seq
wgcna
software error
R
next-gen
updated 2.4 years ago by
Dio
• 0 • written 5.6 years ago by
giuseppe0525
▴ 20
5
votes
17
replies
4.3k
views
Interpreting Genome_Structural_Correction Block_Bootstrap.Py
statistics
encode
10.2 years ago by
14134125465346445
★ 3.6k
3
votes
17
replies
2.9k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing
faire
mapping
3.1 years ago by
boczniak767
▴ 850
0
votes
17
replies
1.5k
views
Transcripts with no read support
RNA-Seq
alignment
assembly
salmon
3.7 years ago by
Dunois
★ 2.5k
12
votes
17
replies
4.9k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python
Newick
phylogenetics
tree
phylogeny
6.6 years ago by
anonymous1192976466
▴ 50
1
vote
17
replies
2.4k
views
Normalizing BLAST results
blast
updated 6.6 years ago by
Biostar
20 • written 6.8 years ago by
db
• 0
2
votes
17
replies
5.1k
views
Coding Potential Calculator (CPC) error
RNA-Seq
updated 6.2 years ago by
h.mon
35k • written 6.2 years ago by
Janey
▴ 30
20
votes
17
replies
3.4k
views
How to add "transcript" feature to a gtf file?
gtf
updated 10 months ago by
1769mkc
★ 1.2k • written 3.3 years ago by
pomodoro_sinensis
▴ 110
0
votes
17
replies
5.0k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 20 months ago by
Ram
43k • written 8.7 years ago by
jigarnt
▴ 30
8
votes
17
replies
4.0k
views
Getting nan value in vcftool relatedness command?
vcftools
relatedness
6.3 years ago by
Sharon
▴ 610
2
votes
17
replies
9.9k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping
genome
fastq
STAR
updated 2.2 years ago by
todd.ugine
• 0 • written 3.4 years ago by
merfer0206
• 0
2
votes
17
replies
4.4k
views
Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
sam
bam
alignment
samtools
updated 10.4 years ago by
Devon Ryan
104k • written 10.4 years ago by
Rohit
★ 1.5k
4
votes
17
replies
2.9k
views
Cufflinks analysis and gffread
RNA-Seq
Assembly
updated 6.5 years ago by
Kevin Blighe
88k • written 6.6 years ago by
qudrat
▴ 100
2
votes
17
replies
2.9k
views
Snakemake Megahit error
megahit
Snakemake
2.5 years ago by
blackadder
▴ 30
6
votes
17
replies
2.4k
views
6 follow
Issue with reverting bam file back to fastq files
next-gen
assembly
genome
alignment
5.9 years ago by
williamsbrian5064
▴ 520
9
votes
17
replies
2.2k
views
Creating intergenic bam file
R
genome
intergenic
alignment
7.8 years ago by
erincyurtman
• 0
1
vote
17
replies
4.3k
views
Error executing bedops convert2bed
bedops
bed
vcf
convert2bed
7.3 years ago by
lakhujanivijay
5.8k
7
votes
17
replies
6.6k
views
HeatMap: how to cluster only the rows and keep order of the heatmap's column labels as same as in the df?
R
gene
genome
5.9 years ago by
WUSCHEL
▴ 760
0
votes
17
replies
3.1k
views
I am not able to let R read my file
R
fasta
updated 3.2 years ago by
Arup Ghosh
3.2k • written 3.2 years ago by
trejomarco6
• 0
0
votes
17
replies
2.8k
views
Fail running blastdb and blastn on my own computer
blast
6.5 years ago by
annette440
• 0
28
votes
17
replies
22k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
2.5 years ago by
Leite
★ 1.3k
3
votes
17
replies
1.6k
views
copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
CNV
DownSample
fastq
copy number not accurate
4.3 years ago by
lffu_0032
▴ 90
5
votes
17
replies
8.7k
views
Removing fastq duplicates
sequence
next-gen
ChIP-Seq
3.5 years ago by
C4
▴ 30
4
votes
17
replies
2.8k
views
Any strategy to find out the reason of having unusual Coefficient of Variation (CV) for gene expression data?
microarray
gene-expression
CV
error
4.9 years ago by
Jurat Shahidin
▴ 100
7
votes
17
replies
3.9k
views
How to find the differences in aligned bam files
RNA-Seq
7.2 years ago by
1769mkc
★ 1.2k
0
votes
17
replies
1.2k
views
Issues while running htseq-count
Candida-glabrata
RNA-seq
htseq-count
4 months ago by
Foad
▴ 10
1
vote
17
replies
5.8k
views
BBMap: Mapping Fails
BBTools
BBMap
Mapping
updated 8.2 years ago by
GenoMax
142k • written 8.2 years ago by
cacampbell
▴ 60
7
votes
16
replies
3.7k
views
How do I get a GFF file
snp
4.9 years ago by
apl00028
▴ 90
0
votes
16
replies
4.6k
views
Issue using MaSuRCA-3.2.6
Assembly
assembler
updated 5.7 years ago by
Biostar
20 • written 5.9 years ago by
Chvatil
▴ 130
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length
Bed
updated 11 months ago by
Ram
43k • written 4.3 years ago by
Ankit
▴ 500
3
votes
16
replies
3.5k
views
FastTree trifurcating Root node
alignment
FastTree
Phylogenetic Tree
5.4 years ago by
Moses
▴ 150
9
votes
16
replies
1.5k
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 3.8 years ago by
lieven.sterck
15k • written 3.8 years ago by
schlogl
▴ 160
2
votes
16
replies
3.1k
views
Enhancing draft genome using 10X data
10X
draft_genome
Assembly
5.8 years ago by
Mostafa
▴ 20
8
votes
16
replies
1.5k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene
next-gen
4.4 years ago by
Chaimaa
▴ 260
9
votes
16
replies
2.0k
views
feature extraction from SNPs in R
R
gene
sequence
SNP
5.5 years ago by
bioinfo456
▴ 150
13
votes
16
replies
7.3k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
5.4 years ago by
DNAngel
▴ 250
1
vote
16
replies
7.1k
views
After sorting bam file not able to index ?
alignment
next-gen
updated 5.3 years ago by
Biostar
20 • written 5.4 years ago by
sunnykevin97
▴ 980
16
votes
16
replies
3.2k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
6.2 years ago by
bioinfo456
▴ 150
1,000 results • Page
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Recent Replies
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file
by
pirku
• 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice
by
GenoMax
142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line
by
Arthur
• 0
If it cans help, I got the same error message : There were errors in the input file (listed above). According to "mainparams" the inp…
Comment: CreateSeuratObject taking very long
by
Nitin Narwade
★ 1.6k
I am not sure whether it will speedup the conversion but you can give it a try. convert your dataframe into a sparse matrix before creatin…
Comment: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 210
The timing for your question is excellent. The fix was released yesterday.
Comment: vcf phasing
by
WouterDeCoster
47k
> I observed that it doesn't phase genotypes labeled as 0/0 How could such a genotype even be phased?
Comment: Super ehancers
by
Oburah
• 0
Well-noted however just wondering what you me by GFF being shorter. Thank you![See the screeshot snap of the gff file][1] [1]: /media/i…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
I know illumina will only give me high-quality contigs. the samples which are to be sequenced with Long_Short read sequence will be used as…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Hi, Thank you for a detailed responce. Let me add some more informations. Long-Read is ~75X coverage. Short-Read is ~100X coverage. **For…
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by
Klaus S
▴ 160
The best is to prune the tree and also the bootstrap trees and afterwards re-assign the bootstrap values to the tree. The bootstrap values …
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Here's a more neat version of the plot generated while writing my dissertation: ![enter image description here][1] [1]: https://raw.gi…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 130
what a pity...
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