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Showing top results for tag: extraction • reset
0
votes
3
replies
222
views
Unable to extract country name from genbank file
Genbank data extraction
updated 7 weeks ago by ★ 2.6k • written 7 weeks ago by • 0
0
votes
0
replies
587
views
Need to extract specific VCF sample IDs from 1000Genomes project in the group 30x 1000 genomes genotypes aligned to gr38
1000genomes extraction vcf data
3 months ago by screadore ▴ 20
1
vote
9
replies
1.8k
views
In R: Print column names if value is greater than a value in a different column.
R data extraction
updated 15 months ago by 8.6k • written 15 months ago by • 0
2
votes
6
replies
755
views
Failure in extracting reads from bam file due to unknown reference
alignment bam extraction reference
20 months ago by marongiu.luigi ▴ 570
2
votes
3
replies
642
views
How can I Extract PMID only for a query in a text file while searching it on NCBI pubmed?
sequence literature extraction alignment next-gen
updated 22 months ago by • 0 • written 2.4 years ago by • 0
4
votes
7
replies
887
views
Extracting contaminated reads from the sequenced data
genome sequencing extraction illumina
updated 2.5 years ago by 104k • written 2.5 years ago by ▴ 50
4
votes
11
replies
1.6k
views
grep/awk issue: can't extract sequences from a fasta file
fasta sequence extraction grep shell
updated 2.7 years ago by 20 • written 3.1 years ago by ▴ 10
0
votes
1
reply
494
views
Features extraction from protein 3D structures
proteins features extraction 3D strcuture
2.7 years ago by biotechuos4 • 0
4
votes
8
replies
4.2k
views
Extract Only Paired-End Reads That Map A Specific Interval
bedtools extraction
updated 2.8 years ago by • 0 • written 8.9 years ago by 9.5k
0
votes
3
replies
638
views
Extract sequences which do not have blast hits
RNA-Seq sequence blast extraction
2.8 years ago by karthic ▴ 110
5
votes
11
replies
2.4k
views
subgraph extraction based on the edges weights and graph connectivity
R graph subgraph extraction weight
updated 3.1 years ago by ▴ 450 • written 3.1 years ago by ▴ 240
0
votes
0
replies
1.1k
views
Extraction of 16S hypervariable regions
16S hypervariable regions software extraction
3.7 years ago by jerald • 0
2
votes
3
replies
1.6k
views
Extracting Protein Sequences
protein sequence extraction
updated 3.9 years ago by 20 • written 9.8 years ago by ▴ 280
12
votes
10
replies
4.8k
views
How to extract contigs from FASTA file which contains specific sequence
fasta contig extraction find
updated 3.9 years ago by 18k • written 6.6 years ago by ★ 1.4k
3
votes
12
replies
1.7k
views
how to extract a random set of SNP from a SNP table
SNP random sample extraction
updated 4.2 years ago by 33k • written 4.2 years ago by ▴ 180
0
votes
0
replies
2.4k
views
SNPSift Genotype Extraction
snpsift genotype extraction
updated 6.2 years ago by 20 • written 6.2 years ago by ▴ 10
6
votes
13
replies
3.4k
views
6 follow
Partial Cds Extraction From Incomplete Transcripts
cds extraction rna
updated 6.9 years ago by 20 • written 9.6 years ago by ▴ 200
1
vote
8
replies
3.8k
views
Get All Alleles Of 1 Column In Bam File
bam position extraction read
updated 7.3 years ago by ▴ 70 • written 9.7 years ago by ▴ 10
0
votes
2
replies
5.3k
views
Motif Extraction Using R Package?
bioinformatics motif extraction r
updated 7.7 years ago by ▴ 70 • written 7.7 years ago by • 0
3
votes
6
replies
4.0k
views
Extracting The Features From Genbank File
genbank feature extraction
updated 7.9 years ago by 20 • written 8.0 years ago by ▴ 640
2
votes
6
replies
3.3k
views
How To Extract Only Geneid From Fasta Header?
sequence extraction fasta perl
updated 8.0 years ago by ★ 1.3k • written 8.0 years ago by ▴ 60
8
votes
3
replies
5.8k
views
A Way To Get Dna Sequence From Specific Coordinates Using An Online Service
sequence extraction
updated 8.2 years ago by 137k • written 8.2 years ago by ★ 4.0k
22
votes
20
replies
4.2k
views
How To Join Text Files By A Certain Column (Accession Id)
extraction
updated 8.5 years ago by ▴ 300 • written 8.5 years ago by ▴ 100
8
votes
6
replies
5.5k
views
Sra Toolkit For Pacbio
sra extraction
updated 8.6 years ago by ▴ 210 • written 8.6 years ago by ★ 3.1k
9
votes
6
replies
1.5k
views
Matching The Entries And Printing Data
sequence extraction id script
updated 8.8 years ago by 9.7k • written 8.8 years ago by ▴ 910
11
votes
16
replies
7.6k
views
6 follow
Help Me Finish This Perl Code To Extract A Column In A Table
perl data extraction
updated 8.8 years ago by ★ 7.4k • written 8.8 years ago by ▴ 50
1
vote
2
replies
2.4k
views
Contig Extraction From .Ace File
assembly extraction metagenomics
updated 8.8 years ago by 4.1k • written 8.8 years ago by • 0
1
vote
3
replies
4.2k
views
[Help]: Extracting Sequence From Fasta Using Blast Informations?
python biopython fasta blast extraction
9.0 years ago by francois.maginiot ▴ 10
24
votes
7
replies
26k
views
How To Extract Set Of Reads From Fastq (Or Eventually Fasta And Qual) Based On List Of Ids?
extraction read 454 fastq fasta
updated 9.2 years ago by 3.0k • written 9.2 years ago by 3.1k
6
votes
4
replies
1.4k
views
Experiment Data
data extraction
updated 9.2 years ago by 8.2k • written 9.2 years ago by ▴ 160
28
votes
6
replies
25k
views
How To Use Bedtools To Extract Promoters From A Mouse Bed File
bedtools bed extraction promoter fasta
updated 9.5 years ago by 11k • written 9.5 years ago by ★ 2.8k
14
votes
12
replies
9.5k
views
7 follow
How To Extract Random Snps From Whole Genome Data?
snp extraction
updated 6 weeks ago by • 0 • written 9.5 years ago by ▴ 40
1
vote
3
replies
2.3k
views
Extract A Subrange Of Sequences From A Genbank File
extraction genbank
updated 9.6 years ago by 137k • written 9.6 years ago by ▴ 50
2
votes
3
replies
1.9k
views
Extraction Of Part Of Different Grp Of Nucleotide Sequence In 10000 Of Sequences.
extraction sequence
updated 9.7 years ago by 5.2k • written 9.9 years ago by • 0
22
votes
11
replies
11k
views
9 follow
Bam : Extract Only Alignment With A Specific Length
bam rna alignment extraction length
updated 9.8 years ago by ▴ 850 • written 9.8 years ago by 9.5k
6
votes
6
replies
1.9k
views
Text Mining: Extracting Some Genes And Some Variations From An Article.
text identifiers extraction variant
updated 10.0 years ago by 4.3k • written 10.0 years ago by 137k
22
votes
5
replies
3.8k
views
Is There Any Tool To Extract Demanded Information From An Asn/Xml File?
xml human gene extraction
updated 10.3 years ago by 3.2k • written 10.9 years ago by ▴ 20
24
votes
11
replies
8.9k
views
7 follow
How To Extract Specific Coordinates From Multifasta File
extraction fasta coordinates
updated 10.4 years ago by ▴ 30 • written 10.4 years ago by ▴ 70
38 results • Page 1 of 1
Recent Votes
Gene Set Enrichment Analysis
Answer: Would this laptop be sufficient for small dataset/sequence analysis?
Answer: What's the biggest thing you dislike about bioinformatics?
Comment: opening downloaded files from STRING protein network without R
Comment: What's the biggest thing you dislike about bioinformatics?
Gene Set Enrichment Analysis
Comment: Removing genes of Seurat object during integration pipeline
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Teacher to WouterDeCoster 45k
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Recent Replies
Answer: Would this laptop be sufficient for small dataset/sequence analysis? by Mensur Dlakic ★ 12k
16 GB of RAM will not cut it for any serious bioinformatics application these days. Doubly so if you choose to run Windows.
Comment: inquiry related to snpsift by Kevin Blighe 75k
I see - thanks. I am not sure that `SnpSift annotate` can do this, but you can first remove the original ID via `bcftools`, as follows: …
Answer: Forum: Job opportunities in Europe, with and without a PhD by Kevin Blighe 75k
South Africa? - very nice. I had been considering moving there, would you believe. There is no correct answer to your question, and one ca…
Comment: inquiry related to snpsift by rheab1230 • 0
the command: java -jar SnpSift.jar annotate dbSnp144.vcf variants.vcf > variants_annotated.vcf I am getting no error. the input file …
Comment: Displaying points which fall outside of the plot window in EnhancedVolcano by os306 ▴ 10
Hi there, just to follow up on this, I used your package to generate my volcano plots and got exactly what I was looking for. I now wish to…
Comment: inquiry related to snpsift by Kevin Blighe 75k
Hi, please show: 1. the command(s) that you are using 2. a sample of your input data 3. a sample of your output data 4. any status, wa…
Comment: opening downloaded files from STRING protein network without R by fionajcunningham • 0
thanks GenoMax I will try this sorry for delay in reply!! Fiona
Comment: What's the biggest thing you dislike about bioinformatics? by WouterDeCoster 45k
The alternative, constant off-by-one errors, aren't my idea of fun either :-)
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
Yeah, you can filter min_cells in Seurat with SCtransform. That would probably change the gene numbers in the SCT assay of the object. I u…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
Doesn't sctransform has a `min_cells` parameter that you could use here? It will only consider genes detected in at least `min_cells` cells…
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
I was thinking of making it an arbitrary cut off of 10 cells, Seurat's documentation uses 3 for reading in a single sample. I believe that …
Answer: How To Split A Bam File By Chromosome by etiennedanis • 0
With samtools v1.11, ```samtools view -b in.bam chr1 > out.bam``` did not work for me. But ```samtools view -b in.bam 1 > out.bam``` wo…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
What is a "few" cells? So how many? You would need to manually calculate the fraction of cells expressing a certain gene. Not sure in which…
Comment: I want to make a graph for conserved regions by sa.youssef • 0
Thanks so much, it is a great suggestion. may I ask you if you know a way to visualize the results of these data in my report? as we are wo…
Comment: Minfi - estimateCellCounts by Papyrus ★ 1.1k
I understand that you have whole blood samples and that's why you expect them to have more granulocytes? You could also try the [ENmix][1] …
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