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1,000 results • Page
4 of 20
Sort: Votes
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Views
Votes
Replies
9
votes
13
replies
3.3k
views
Python Script to map reads to reference sequence
sequence
python
mapping
script
reference sequence
5.0 years ago by
Fid_o
▴ 40
9
votes
5
replies
1.2k
views
how to retrieve all proteins related to cancer
proteins
7.9 years ago by
Learner
▴ 280
9
votes
13
replies
1.6k
views
SNP's and Gene?
SNP
gene
4.5 years ago by
imgapgenomika
▴ 10
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
9
votes
10
replies
2.2k
views
[solved] Convert fold changes of multiple transcripts of a given gene to a single value characterising this gene
RNA-Seq
7.6 years ago by
biostart
▴ 370
9
votes
10
replies
3.4k
views
generation of heat map by excel data.
R
excel
heatmap
updated 5.8 years ago by
Ram
43k • written 5.8 years ago by
abhilashreddy495
▴ 10
9
votes
11
replies
6.6k
views
microRNA Illumina Sequencing - Very low alignment rate
sequencing
Assembly
RNA-Seq
updated 2.2 years ago by
Ram
43k • written 9.7 years ago by
wynstep
▴ 90
9
votes
6
replies
1.3k
views
Genotype meaning
genotype
BL21
2.8 years ago by
A_heath
▴ 160
9
votes
10
replies
1.8k
views
How to use Poisson distribution to get meaningful expression counts?
statistics
rna-seq
updated 2.7 years ago by
i.sudbery
19k • written 2.8 years ago by
c_u
▴ 520
9
votes
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
4 months ago by
analyst
▴ 20
9
votes
12
replies
1.4k
views
Copy number variations analysis
R
CNV
updated 4.4 years ago by
zx8754
11k • written 4.4 years ago by
rprog008
▴ 70
9
votes
7
replies
1.2k
views
Reference genome location
reference
positions
FASTA
alignment
genome
updated 15 months ago by
barslmn
★ 2.1k • written 15 months ago by
Batel
• 0
9
votes
11
replies
4.4k
views
please someone help me with running mirdeep2
software error
mirdeep2
perl
7.6 years ago by
zizigolu
★ 4.3k
9
votes
5
replies
711
views
Prophage prediction tool
prophage
PHASTER
prediction
updated 9 months ago by
GenoMax
141k • written 9 months ago by
A_heath
▴ 160
9
votes
6
replies
3.4k
views
SOAPaligner 2.21 - does it replace all Ns by Gs in reads?
Soapaligner
alignment
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
Philipp Bayer
8.3k
9
votes
7
replies
1.1k
views
ChIP-seq; investigate binding within region of tRNA genes
tRNA
ChIP
nf-core
ChIP-seq
updated 23 months ago by
Ram
43k • written 24 months ago by
2138493o
▴ 20
9
votes
27
replies
7.5k
views
How do I use Glimmer 3.02?
sequencing
updated 5.2 years ago by
ojelizodun
• 0 • written 6.1 years ago by
nattzy94
▴ 50
9
votes
13
replies
2.4k
views
Reannotating a gene: Identifying translation and transcription start sites
RNA-Seq
genome
gene
7.3 years ago by
rh5118
▴ 40
9
votes
14
replies
4.3k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
hothriananya
▴ 70
9
votes
2
replies
571
views
Answer needed urgently
Deep
updated 19 months ago by
Mensur Dlakic
★ 27k • written 19 months ago by
Deepak
• 0
9
votes
12
replies
7.3k
views
How to align reads on reference using python?
genome
sequence
gene
sequencing
updated 5.4 years ago by
WouterDeCoster
47k • written 5.4 years ago by
doramora
▴ 10
9
votes
10
replies
2.5k
views
why there is 0/0 genotyp in VCF file?
VCF
GATK
Variant
4.7 years ago by
star
▴ 350
9
votes
3
replies
7.2k
views
Statistical Distributions In Rna-Seq Data Analysis
statistics
rna
updated 5.1 years ago by
Biostar
20 • written 12.1 years ago by
Ngsnewbie
▴ 380
9
votes
7
replies
1.9k
views
Is the sequence quality good enough?
WGS
HISEQ4000
QC
5.9 years ago by
BioinfGuru
★ 1.7k
9
votes
7
replies
3.3k
views
Aligning Miseq With Deletions >10 Bases
alignment
miseq
next-gen
updated 10.7 years ago by
Biostar
20 • written 11.3 years ago by
Leszek
4.2k
8
votes
16
replies
1.4k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene
next-gen
4.3 years ago by
Chaimaa
▴ 260
8
votes
8
replies
1.8k
views
Sequence alignment algorithm for big size genes in MATLAB
alignment
Matlab
next-gen
6.9 years ago by
r.tor
▴ 50
8
votes
7
replies
1.0k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf
VEP
10 months ago by
Jeremy Leipzig
22k
8
votes
3
replies
3.3k
views
which tool is used for separating forward and reverse from paired end fastq
Assembly
6.8 years ago by
ranjini.shakthi
• 0
8
votes
10
replies
651
views
bash script
whole-genome-sequencing
updated 3 days ago by
Ram
43k • written 10 days ago by
bestone
▴ 30
8
votes
6
replies
2.6k
views
for low coverage RNAseq how many reads assigned is the bare minimum for differential gene expression analysis
RNA-Seq
5.2 years ago by
senowinski
▴ 30
8
votes
14
replies
6.0k
views
Error in BWA-MEM running in linux
RNA-Seq
BWA-MEM
alignment
updated 5.9 years ago by
GenoMax
141k • written 5.9 years ago by
modarzi
▴ 170
8
votes
11
replies
5.7k
views
RNASeq gender identification
RNA-Seq
6.6 years ago by
popayekid55
▴ 110
8
votes
4
replies
2.2k
views
Use Of Terms In Genome-Wide Analysis: Phenotype / Functionality / Fitness
12.7 years ago by
2184687-1231-83-
★ 5.1k
8
votes
5
replies
3.1k
views
7 follow
What is the best way to merge multiple fasta files containing contigs?
Assembly
Anvi’o
fasta
updated 5.2 years ago by
zx8754
11k • written 5.2 years ago by
anastasia.gs17
• 0
8
votes
4
replies
855
views
Correlation network analysis
rna-seq
3.3 years ago by
Lepomis_8
▴ 30
8
votes
8
replies
2.7k
views
Making chain files
Assembly
genome
alignment
sequence
updated 4.7 years ago by
Biostar
20 • written 4.8 years ago by
mc2548
▴ 50
8
votes
11
replies
1.9k
views
Sending files to Galaxy
Galaxy
fastq
7.6 years ago by
statfa
▴ 760
8
votes
7
replies
3.8k
views
6 follow
Compatibility between my reference genome and GTF file
rna-seq
hisat2
alignment
reference genome
5.6 years ago by
Batu
▴ 250
8
votes
1
reply
1.5k
views
Genome Sequencing And Evolutionary History
evolution
updated 10.2 years ago by
Neilfws
49k • written 10.2 years ago by
robjohn7000
▴ 110
8
votes
11
replies
1.9k
views
using STAR instead of HISAT2
STAR
updated 21 months ago by
Ram
43k • written 21 months ago by
Chris
▴ 260
8
votes
4
replies
15k
views
Use of if-else statement in snakemake rule
snakemake
if-else
python
updated 4.4 years ago by
schroder.julia
• 0 • written 6.8 years ago by
Jokhe
▴ 140
8
votes
9
replies
3.0k
views
error in rstudio
csv
matrix
rstudio
updated 18 months ago by
Ram
43k • written 8.7 years ago by
zizigolu
★ 4.3k
8
votes
14
replies
2.6k
views
RNA-Seq analysis with standard p-value
RNA-Seq
7.2 years ago by
####
▴ 220
8
votes
7
replies
4.0k
views
Error with Bowtie 2
bowtie2
alignment
6.9 years ago by
valerie
▴ 100
8
votes
7
replies
6.9k
views
I got low overall alignment rate running HiSAT2
RNA-Seq
hisat
hisat2
alignment
7.6 years ago by
sslee1015
• 0
8
votes
11
replies
4.9k
views
Increasing kmer limit in SPAdes
Assembly
Bacterial
Spades
Velvet
7.7 years ago by
rrcutler
▴ 120
8
votes
5
replies
1.9k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 7 months ago by
Ram
43k • written 2.5 years ago by
A_heath
▴ 160
8
votes
30
replies
5.1k
views
Per Base Sequence Content
sequencing
fastqc
genome
sequence
updated 4.1 years ago by
wm
▴ 550 • written 4.1 years ago by
Researcher
▴ 20
8
votes
11
replies
4.1k
views
STAR can not detect this chimeric read
RNA-Seq
fusion
STAR
updated 7.4 years ago by
Biostar
20 • written 7.6 years ago by
Nicolas Rosewick
10k
1,000 results • Page
4 of 20
Recent Votes
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Answer: Downloaded pdb's on rcsb.org
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Recent Awards •
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141k
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★ 1.2k
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Recent Replies
Comment: Removing duplicates
by
joe
▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you very much
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool
by
GenoMax
141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
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