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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
16
votes
21
replies
2.2k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
7.5 years ago by
Farbod
★ 3.4k
6
votes
21
replies
2.8k
views
How to evaluate the similarity of genes between two sample
RNA-Seq
differential
updated 5.6 years ago by
Biostar
20 • written 5.7 years ago by
afli
▴ 190
9
votes
20
replies
4.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 13 months ago by
Ram
43k • written 5.7 years ago by
marongiu.luigi
▴ 710
0
votes
20
replies
1.6k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
6 months ago by
langziv
▴ 50
6
votes
20
replies
6.4k
views
filling of missing genotype information in merged variant call vcf file
SNP
5.9 years ago by
princy149
▴ 80
22
votes
20
replies
2.5k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 12 months ago by
Ram
43k • written 7.8 years ago by
Farbod
★ 3.4k
8
votes
20
replies
2.6k
views
Getting read depth for normal and tumour
R
WGS
vcf
5.0 years ago by
zizigolu
★ 4.3k
5
votes
20
replies
8.3k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
7.7 years ago by
varsha619
▴ 90
5
votes
20
replies
4.1k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 18 months ago by
Ram
43k • written 8.7 years ago by
Hans
▴ 140
4
votes
20
replies
1.9k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
4.3 years ago by
schlogl
▴ 160
8
votes
20
replies
2.9k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
6.3 years ago by
corend
▴ 70
8
votes
20
replies
2.5k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 23 months ago by
Ram
43k • written 5.7 years ago by
Bara'a
▴ 270
2
votes
20
replies
2.3k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
7 months ago by
Maxine
▴ 40
6
votes
19
replies
2.8k
views
Clustering for Single-cell RNA-seq Data
clustering
R
single-cell
4.7 years ago by
aloke205
▴ 40
3
votes
19
replies
1.5k
views
Systematic errors at the end and beginning of reads in NGS panels
NGS
error
panels
sequencing
updated 9 months ago by
Asaf
10k • written 9 months ago by
captainlabman
▴ 20
9
votes
19
replies
2.3k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
4.2 years ago by
schlogl
▴ 160
6
votes
19
replies
1.7k
views
Fastq header modification
sequence
next-gen
updated 6.1 years ago by
Ram
43k • written 6.1 years ago by
Guillaume
• 0
3
votes
19
replies
6.0k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 4.9 years ago by
finswimmer
16k • written 4.9 years ago by
sruthi
▴ 40
5
votes
19
replies
3.9k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 3 months ago by
ATpoint
81k • written 4.9 years ago by
ta_awwad
▴ 340
22
votes
19
replies
3.2k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.5 years ago by
zizigolu
★ 4.3k
5
votes
19
replies
1.7k
views
how I can come up with a permanent error
R
software error
7.0 years ago by
zizigolu
★ 4.3k
0
votes
19
replies
2.8k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
2.7 years ago by
rheab1230
▴ 140
0
votes
19
replies
3.8k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
6.3 years ago by
jaqx008
▴ 110
15
votes
19
replies
1.9k
views
trimmomaric command for a fasta file?
trimmomatic
updated 6.0 years ago by
Ram
43k • written 6.0 years ago by
Nadin.asal
• 0
0
votes
19
replies
1.9k
views
scatterplot in R
microarray
expression
gene
updated 18 months ago by
Ram
43k • written 18 months ago by
bioinformatics
▴ 40
7
votes
19
replies
2.9k
views
mapping script process sleeping on server.
alignment
updated 23 months ago by
Ram
43k • written 9.1 years ago by
lvogel
▴ 30
4
votes
19
replies
3.1k
views
Use machine learning as classifier
R
rRNA
16S
18S
ITS
updated 6.6 years ago by
Biostar
20 • written 6.8 years ago by
cool.abbecker
▴ 30
7
votes
19
replies
7.0k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray
R
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
mheiser1
▴ 10
17
votes
19
replies
2.8k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.6 years ago by
Gian77
▴ 60
18
votes
19
replies
2.3k
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 16 months ago by
Ram
43k • written 5.3 years ago by
rbkh09
• 0
13
votes
19
replies
5.3k
views
bbmerge not joining paired-end reads
bbmerge
alignment
6.4 years ago by
bioplanet
▴ 60
0
votes
19
replies
1.5k
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
4.4 years ago by
marongiu.luigi
▴ 710
0
votes
19
replies
9.5k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.9 years ago by
seta
★ 1.9k
1
vote
19
replies
2.0k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
5.4 years ago by
eozcan
▴ 10
0
votes
19
replies
1.4k
views
map fasts files
RNA-Seq
FASTQ
R
6.2 years ago by
Learner
▴ 280
1
vote
19
replies
7.0k
views
Conda install package - different internals
R
software error
updated 4.7 years ago by
Biostar
20 • written 4.7 years ago by
lihe.liu
▴ 30
1
vote
19
replies
839
views
Matching transcriptomic data to clinical data
R
updated 10 weeks ago by
Ram
43k • written 11 weeks ago by
Khadija
▴ 10
10
votes
19
replies
3.4k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 2.9 years ago by
GenoMax
141k • written 2.9 years ago by
matt
▴ 20
2
votes
18
replies
6.2k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
7.4 years ago by
Sumit Paliwal
▴ 40
2
votes
18
replies
2.4k
views
I need help in this
gene
weblems
alignment
updated 20 months ago by
Ram
43k • written 8.3 years ago by
efosa15
• 0
1
vote
18
replies
1.7k
views
Find tissues that are functionally related
tissue
functionally-related
gene-expression
updated 4.6 years ago by
Biostar
20 • written 4.6 years ago by
Natasha
▴ 40
14
votes
18
replies
2.1k
views
Clustering in single cell
seurat
single-cell
updated 6 months ago by
e.r.zakiev
▴ 190 • written 6 months ago by
Chris
▴ 260
5
votes
18
replies
6.7k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
4.4 years ago by
michelle.piquet
▴ 60
7
votes
18
replies
8.5k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
hana
▴ 190
1
vote
18
replies
2.7k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
7.7 years ago by
Tom
▴ 40
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
16 days ago by
b.contreras.moreira
▴ 150
2
votes
18
replies
2.7k
views
Bwa on multiple processor
np
mpirun
bwa
alignment
2.3 years ago by
shivangi.agarwal800
▴ 120
4
votes
18
replies
17k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 3.5 years ago by
Biostar
20 • written 5.7 years ago by
Shelle
▴ 30
0
votes
18
replies
1.8k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 7 months ago by
GenoMax
141k • written 7 months ago by
Apex92
▴ 280
7
votes
18
replies
4.9k
views
Fold change UP and Down in dplyr calculation
R
6.7 years ago by
1769mkc
★ 1.2k
1,000 results • Page
2 of 20
Recent Votes
Answer: How to compare the quality of assemblies
How to compare the quality of assemblies
A: Best strategy for gene annotation for de novo genome assembly without RNA-seq da
Comment: Questions about a bug when transferring cram file to bam file
Answer: Problem with Mirdeep2 and Randfold output
Comment: Trying to write bwa mem -> samtools view -> samtools sort loop
C: Extract fasta sequences from a file using a list in another file.
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141k
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jkbonfield
★ 1.2k
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to
yueli7
▴ 250
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8.5k
Recent Replies
Answer: How to compare the quality of assemblies
by
shelkmike
★ 1.2k
Since BUSCO results are almost identical but the assembly sizes differ significantly, I suppose that the difference between the assemblies …
Comment: differential gene expression analysis when not all samples have an untreated cou
by
nhaus
▴ 300
Thank you very much for your answer, that was very helpful! > Impossible to say. It depends on your data, particularly on how the donors …
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
bk11
★ 2.3k
This could be because they are probably merging two or more datasets. If you are merging two or more datasets, it will be very important th…
Answer: Problem with Mirdeep2 and Randfold output
by
otieno43
▴ 30
I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file
by
GenoMax
141k
Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle
by
Ram
43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle
by
Joseph
• 0
Hi, Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome
by
colindaven
6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Elisabeth Gasteiger
★ 2.4k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates
by
valentinatsar
• 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How to compare the quality of assemblies
by
GenoMax
141k
Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
Comment: Korean human genome reference file
by
GenoMax
141k
From NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001712695.1/ Use the `Download` button or `curl/datasets`.
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