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1,000 results • Page
3 of 20
Sort: Votes
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Views
Votes
Replies
10
votes
15
replies
5.4k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
6.3 years ago by
Farbod
★ 3.4k
10
votes
3
replies
1.2k
views
how to create new file
r
updated 6.4 years ago by
GenoMax
127k • written 6.4 years ago by
forever
▴ 80
9
votes
13
replies
2.6k
views
Python Script to map reads to reference sequence
sequence
python
mapping
script
reference sequence
3.9 years ago by
Fid_o
▴ 40
9
votes
5
replies
1.0k
views
how to retrieve all proteins related to cancer
proteins
6.9 years ago by
Learner
▴ 260
9
votes
7
replies
2.9k
views
Aligning Miseq With Deletions >10 Bases
alignment
miseq
next-gen
updated 9.7 years ago by
Biostar
20 • written 10.2 years ago by
Leszek
4.2k
9
votes
13
replies
1.2k
views
SNP's and Gene?
SNP
gene
3.4 years ago by
imgapgenomika
▴ 10
9
votes
10
replies
1.6k
views
why there is 0/0 genotyp in VCF file?
VCF
GATK
Variant
3.6 years ago by
star
▴ 330
9
votes
16
replies
892
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 2.6 years ago by
lieven.sterck
14k • written 2.6 years ago by
schlogl
▴ 130
9
votes
27
replies
6.0k
views
How do I use Glimmer 3.02?
sequencing
updated 4.2 years ago by
ojelizodun
• 0 • written 5.0 years ago by
nattzy94
▴ 50
9
votes
16
replies
1.3k
views
feature extraction from SNPs in R
R
gene
sequence
SNP
4.4 years ago by
bioinfo456
▴ 150
9
votes
19
replies
1.6k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
3.2 years ago by
schlogl
▴ 130
9
votes
7
replies
783
views
Reference genome location
reference
positions
FASTA
alignment
genome
updated 11 weeks ago by
barslmn
★ 1.4k • written 12 weeks ago by
Batel
• 0
9
votes
2
replies
5.0k
views
Biopython Import Error
biopython
updated 10.8 years ago by
Michael Kuhn
5.0k • written 10.8 years ago by
angeles.sepulvedap
• 0
9
votes
2
replies
362
views
Answer needed urgently
Deep
updated 6 months ago by
Mensur Dlakic
★ 23k • written 6 months ago by
Deepak
• 0
9
votes
10
replies
1.2k
views
How to use Poisson distribution to get meaningful expression counts?
statistics
rna-seq
updated 20 months ago by
i.sudbery
16k • written 20 months ago by
c_u
▴ 510
9
votes
11
replies
4.0k
views
please someone help me with running mirdeep2
software error
mirdeep2
perl
6.5 years ago by
fi1d18
★ 4.1k
9
votes
13
replies
12k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
3.6 years ago by
Arindam Ghosh
▴ 470
9
votes
13
replies
2.1k
views
Reannotating a gene: Identifying translation and transcription start sites
RNA-Seq
genome
gene
6.2 years ago by
rh5118
▴ 40
9
votes
1
reply
5.4k
views
Why does MACS2 report multiple records for the same peak region?
ChIP-Seq
macs
macs2
updated 7 months ago by
Ram
38k • written 7.4 years ago by
James Ashmore
★ 3.4k
9
votes
4
replies
5.2k
views
How to analyse normalized read count?
RNA-Seq
R
updated 11 weeks ago by
Ram
38k • written 7.8 years ago by
pbio
▴ 150
9
votes
9
replies
1.4k
views
Which hg38 file?
reference
hg38
NCBI
updated 7 months ago by
appropiate
▴ 80 • written 7 months ago by
amy__
▴ 50
9
votes
13
replies
2.0k
views
qRT-PCR data analysis steps and workflow
qRT-PCR
Reference genes
Normalization
DeltaCt
FC
4.1 years ago by
mohammedtoufiq91
▴ 210
9
votes
1
reply
3.2k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq
qc
updated 7 months ago by
Ram
38k • written 7.8 years ago by
Niek De Klein
★ 2.6k
9
votes
14
replies
2.4k
views
vcf to xls wrong columns
vcf
6.6 years ago by
cristina_sabiers
▴ 110
9
votes
7
replies
3.2k
views
How to use Galaxy to obtain read counts from SRA files
Galaxy
read count
SRA file
6.5 years ago by
statfa
▴ 700
9
votes
2
replies
2.8k
views
GEOquery Problems to Get GEO dataset
Geoquery
7.0 years ago by
Shicheng Guo
★ 9.3k
9
votes
9
replies
3.6k
views
ATAC-seq TSS profile plot interpretation
ATAC-seq
TSS
V-plot
3.3 years ago by
nanoide
▴ 100
9
votes
5
replies
4.7k
views
Binning of reads vs. binning of contigs in metagenomics
Binning
Metagenomics
4.3 years ago by
vijinim
▴ 100
9
votes
4
replies
406
views
RNA seq, secreted protein
protein
gene
secreted
updated 3 months ago by
Joe
20k • written 3 months ago by
Rob
▴ 160
9
votes
4
replies
20k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage
depth
read depth
5.9 years ago by
ariel.balter
▴ 190
9
votes
14
replies
3.7k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 12 months ago by
Ram
38k • written 8.2 years ago by
hothriananya
▴ 70
9
votes
4
replies
1.1k
views
Is there any method to run tophat ?
RNA-Seq
updated 4.6 years ago by
Biostar
20 • written 4.7 years ago by
Chan
• 0
9
votes
4
replies
1.5k
views
On which branch in bioinformatics should a cancer researcher focus on ?
cancer
bioinformatics
6.6 years ago by
Bilal
▴ 60
9
votes
12
replies
5.9k
views
How to align reads on reference using python?
genome
sequence
gene
sequencing
updated 4.3 years ago by
WouterDeCoster
47k • written 4.3 years ago by
doramora
▴ 10
9
votes
13
replies
2.0k
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq
DESeq2
updated 23 months ago by
Ram
38k • written 23 months ago by
sumitguptabt
▴ 30
9
votes
6
replies
795
views
Genotype meaning
genotype
BL21
20 months ago by
A_heath
▴ 120
9
votes
17
replies
1.8k
views
Creating intergenic bam file
R
genome
intergenic
alignment
6.6 years ago by
erincyurtman
• 0
9
votes
13
replies
12k
views
Sort bam file by coordinates using samtools
sequencing
next-gen
gene
rna-seq
Tool
updated 4.5 years ago by
finswimmer
16k • written 4.5 years ago by
Shahzad
▴ 30
9
votes
7
replies
687
views
ChIP-seq; investigate binding within region of tRNA genes
tRNA
ChIP
nf-core
ChIP-seq
updated 10 months ago by
Ram
38k • written 11 months ago by
2138493o
▴ 20
9
votes
11
replies
6.8k
views
8 follow
Extremely low mapping rates with bowtie2
alignment
next-gen
updated 5.4 years ago by
Biostar
20 • written 5.5 years ago by
Sachin
▴ 10
9
votes
7
replies
1.7k
views
Sorting BLAST output files together?
blast
6.9 years ago by
zgayk
▴ 90
9
votes
3
replies
6.8k
views
Statistical Distributions In Rna-Seq Data Analysis
statistics
rna
updated 4.0 years ago by
Biostar
20 • written 11.0 years ago by
Ngsnewbie
▴ 380
9
votes
20
replies
3.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 5 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
9
votes
7
replies
4.8k
views
How to combine a different sources of pathway database (KEGG, BioCarta) for Pathway analysis.
Pathway
enrichment analysis
GWAS
pathway analysis
6.8 years ago by
kmsh410
▴ 40
9
votes
16
replies
2.9k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 5 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
9
votes
13
replies
1.3k
views
Archeological DNA sample - how to analyze
unmapped
paleogenomics
archeogenomics
Assembly
14 months ago by
Aruna
▴ 30
9
votes
13
replies
13k
views
GC Content of Fasta file --- Python Help
sequence
6.1 years ago by
Patrick Brennan
▴ 50
9
votes
6
replies
3.0k
views
SOAPaligner 2.21 - does it replace all Ns by Gs in reads?
Soapaligner
alignment
updated 17 months ago by
Ram
38k • written 8.8 years ago by
Philipp Bayer
7.7k
9
votes
10
replies
1.8k
views
About GATK4 Mutect2 runtime (Whole Exome seq)
GATK
Whole Exome Sequencing
Mutect2
2.2 years ago by
kwanghoon
▴ 20
9
votes
9
replies
1.1k
views
Convert mouse amino acid location to genomic location
genome
gene
3.8 years ago by
L. A. Liggett
▴ 120
1,000 results • Page
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A: In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
smoothing or binning bigWig file
List of Ongoing and Planned Long Read Sequencing studies?
Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Answer: Read lengths greater than insert length
A: Changing Output From Gene ID to Symbol When Running findMarkers from Scran
Answer: BLAST Database error: No alias or index file found for nucleotide database
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Comment: split fasta file to train deep learning model
by
shenwei356
7.9k
Excluding sequences containing any letter not belonging to the 20 [amino acids letters](https://github.com/shenwei356/bio/blob/master/seq/a…
Comment: split fasta file to train deep learning model
by
pinheirofabiano
▴ 10
@shenwei356, thank you very much for your help, perfect! But now I realized that some fasta sequences contain the letter "B", which is ou…
Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
by
Mensur Dlakic
★ 23k
I think it depends on the speed of your local disks and the memory amount. On a single node, breaking up the database doesn't sound like a …
Comment: Sample size for population genetics
by
Jeremy Leipzig
21k
Other populations just make the model harder to generalize, not easier.
Comment: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
by
Vincent Laufer
★ 2.5k
i think there is some of that - my most upvoted comment of all time was a dismissive comment i made while extremely tired. for context i ha…
Comment: Molecular biologist / clinical pharmacologist (f/m/d)
by
Jeremy
▴ 770
Is this job on site in Vienna or remote?
Comment: smoothing or binning bigWig file
by
rls_08
▴ 40
if you use bigwigCompare , that would not create a sliding window, but instead, it will output the mean for each bin, according to the -bin…
Comment: Sample size for population genetics
by
zimmer.schweiz
• 0
Thank you so much for your answer. For common polygenic diseases, would it make sense to increase the number of populations sampled, in ord…
Answer: Sample size for population genetics
by
Jeremy Leipzig
21k
For a rare penetrant monogenic disease? A few cases. For a common polygenic disease or trait? 500k-10M
Answer: using GRanges metadata to constrain overlap searches between objects
by
seidel
11k
Rather than do all overlaps all the time for all samples, why not restrict the data by sample when you can. The code below works about 4 ti…
Comment: How to get gene from PSIBLAST resuts
by
Tom
• 0
Hello, thank you for your answer, I have a question, Why the information from the GFF file and from the feature table is different? I see …
Comment: SNP ID (rsID) to Chr no. and Position
by
Jewahir
• 0
Yeah, thank you for that!!
Comment: 1000 genomes hg38 with dbSNP rsid
by
Ram
38k
It should be pretty straightforward. Just to save you some pain, run these on the 1000g VCF once you download it: 1. `vt decompose -s` to …
Comment: 1000 genomes hg38 with dbSNP rsid
by
Vince
▴ 150
Yeah, I had some hope that I wouldn't need to mess with doing this ...
Answer: counting the unmapped reads
by
chemkhi.ali13
• 0
> Hi all, > > I have a sam file, my supervisor asked me to count the number of > unmapped reads, which command I should use? > > sam…
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