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Showing top results for tag: extraction • reset
0
votes
3
replies
302
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Unable to extract country name from genbank file
Genbank data extraction
updated 3 months ago by ★ 2.7k • written 3 months ago by • 0
0
votes
0
replies
615
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
5 months ago by screadore ▴ 20
1
vote
9
replies
2.2k
views
In R: Print column names if value is greater than a value in a different column.
R data extraction
updated 17 months ago by 8.6k • written 17 months ago by • 0
2
votes
6
replies
862
views
Failure in extracting reads from bam file due to unknown reference
alignment bam extraction reference
22 months ago by marongiu.luigi ▴ 580
2
votes
3
replies
696
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 2.0 years ago by • 0 • written 2.6 years ago by • 0
4
votes
7
replies
944
views
Extracting contaminated reads from the sequenced data
genome sequencing extraction illumina
updated 2.7 years ago by 107k • written 2.7 years ago by ▴ 50
4
votes
11
replies
1.7k
views
grep/awk issue: can't extract sequences from a fasta file
fasta sequence extraction grep shell
updated 2.9 years ago by 20 • written 3.3 years ago by ▴ 10
0
votes
1
reply
521
views
Features extraction from protein 3D structures
proteins features extraction 3D strcuture
2.9 years ago by biotechuos4 • 0
4
votes
8
replies
4.3k
views
Extract Only Paired-End Reads That Map A Specific Interval
bedtools extraction
updated 3.0 years ago by • 0 • written 9.1 years ago by 9.6k
0
votes
3
replies
681
views
Extract sequences which do not have blast hits
RNA-Seq sequence blast extraction
3.0 years ago by karthic ▴ 110
5
votes
11
replies
2.5k
views
subgraph extraction based on the edges weights and graph connectivity
R graph subgraph extraction weight
updated 3.2 years ago by ▴ 450 • written 3.2 years ago by ▴ 260
0
votes
0
replies
1.1k
views
Extraction of 16S hypervariable regions
16S hypervariable regions software extraction
3.9 years ago by jerald • 0
2
votes
3
replies
1.6k
views
Extracting Protein Sequences
protein sequence extraction
updated 4.1 years ago by 20 • written 10.0 years ago by ▴ 280
12
votes
10
replies
4.9k
views
How to extract contigs from FASTA file which contains specific sequence
fasta contig extraction find
updated 4.1 years ago by 18k • written 6.7 years ago by ★ 1.4k
3
votes
12
replies
1.8k
views
how to extract a random set of SNP from a SNP table
SNP random sample extraction
updated 4.4 years ago by 33k • written 4.4 years ago by ▴ 180
0
votes
0
replies
2.5k
views
SNPSift Genotype Extraction
snpsift genotype extraction
updated 6.3 years ago by 20 • written 6.4 years ago by ▴ 10
6
votes
13
replies
3.5k
views
6 follow
Partial Cds Extraction From Incomplete Transcripts
cds extraction rna
updated 7.1 years ago by 20 • written 9.8 years ago by ▴ 200
1
vote
8
replies
3.9k
views
Get All Alleles Of 1 Column In Bam File
bam position extraction read
updated 7.5 years ago by ▴ 70 • written 9.9 years ago by ▴ 10
0
votes
2
replies
5.4k
views
Motif Extraction Using R Package?
bioinformatics motif extraction r
updated 7.8 years ago by ▴ 70 • written 7.8 years ago by • 0
3
votes
7
replies
4.1k
views
Extracting The Features From Genbank File
genbank feature extraction
updated 2 days ago by • 0 • written 8.1 years ago by ▴ 650
2
votes
6
replies
3.3k
views
How To Extract Only Geneid From Fasta Header?
sequence extraction fasta perl
updated 8.2 years ago by ★ 1.3k • written 8.2 years ago by ▴ 60
10
votes
3
replies
6.0k
views
A Way To Get Dna Sequence From Specific Coordinates Using An Online Service
sequence extraction
updated 8.3 years ago by 138k • written 8.3 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 8.6 years ago by ▴ 300 • written 8.6 years ago by ▴ 100
8
votes
6
replies
5.6k
views
Sra Toolkit For Pacbio
sra extraction
updated 8.8 years ago by ▴ 210 • written 8.8 years ago by ★ 3.1k
9
votes
6
replies
1.6k
views
Matching The Entries And Printing Data
sequence extraction id script
updated 8.9 years ago by 9.9k • written 8.9 years ago by ▴ 930
11
votes
16
replies
7.7k
views
6 follow
Help Me Finish This Perl Code To Extract A Column In A Table
perl data extraction
updated 9.0 years ago by ★ 7.4k • written 9.0 years ago by ▴ 50
1
vote
2
replies
2.4k
views
Contig Extraction From .Ace File
assembly extraction metagenomics
updated 9.0 years ago by 4.1k • written 9.0 years ago by • 0
1
vote
3
replies
4.3k
views
[Help]: Extracting Sequence From Fasta Using Blast Informations?
python biopython fasta blast extraction
9.2 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 9.4 years ago by 3.0k • written 9.4 years ago by 3.1k
6
votes
4
replies
1.4k
views
Experiment Data
data extraction
updated 9.4 years ago by 8.3k • written 9.4 years ago by ▴ 160
28
votes
6
replies
26k
views
How To Use Bedtools To Extract Promoters From A Mouse Bed File
bedtools bed extraction promoter fasta
updated 9.6 years ago by 11k • written 9.6 years ago by ★ 2.8k
14
votes
12
replies
9.9k
views
7 follow
How To Extract Random Snps From Whole Genome Data?
snp extraction
updated 3 months ago by • 0 • written 9.7 years ago by ▴ 40
1
vote
3
replies
2.4k
views
Extract A Subrange Of Sequences From A Genbank File
extraction genbank
updated 9.7 years ago by 138k • written 9.7 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 9.9 years ago by 5.2k • written 10.1 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 10.0 years ago by ▴ 850 • written 10.0 years ago by 9.6k
6
votes
6
replies
1.9k
views
Text Mining: Extracting Some Genes And Some Variations From An Article.
text identifiers extraction variant
updated 10.2 years ago by 4.3k • written 10.2 years ago by 138k
22
votes
5
replies
3.9k
views
Is There Any Tool To Extract Demanded Information From An Asn/Xml File?
xml human gene extraction
updated 10.5 years ago by 3.2k • written 11.0 years ago by ▴ 20
24
votes
11
replies
9.0k
views
7 follow
How To Extract Specific Coordinates From Multifasta File
extraction fasta coordinates
updated 10.6 years ago by ▴ 30 • written 10.6 years ago by ▴ 70
38 results • Page 1 of 1
Recent Votes
Answer: Are alternative splicing analysis and differential expression analysis of RNA-se
Answer: Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
Comment: Misuse of RPKM or TPM normalization when comparing across samples and sequencing
Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols
Answer: Misuse of RPKM or TPM normalization when comparing across samples and sequencing
A: How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?
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Recent Replies
Answer: ABOUT affymetrix genotyping console (GTC) software and TCGA CNV workflow by xingyu • 0
I still have questions of the log2 ratio value of GTC and DNAcopy. It's noticeable that DNAcopy's log2 ratio value is continuous, but GTC's…
Comment: Problem loading my multifasta by GenoMax 107k
> Invalid msa or the file does not exist! Looks like the program needs a multiple sequence alignment (MSA) file NOT a simple multi-fasta f…
Comment: Misuse of RPKM or TPM normalization when comparing across samples and sequencing by Gordon Smyth ★ 3.4k
There is another subtlety here to do with correction for gene length in the RPKM and TPM measures. Log-counts-per-million performs quite re…
Answer: Create genome-unique intervals from overlapping records in a bed file by Alex Reynolds 33k
You could use [BEDOPS][1] `bedops --partition` to easily [calculate disjoint elements from a set of overlapping elements][2]. Then you co…
Answer: What is the Sleuth intercept and how can Sleuth be used when you have >2 treatme by bkleiboeker ▴ 20
https://github.com/pachterlab/sleuth/issues/156
Comment: filtering and converting data frame to table by Papyrus ★ 1.3k
If the string before the "." is always the same, you can do `substr(dataframe$gene_name,5,999)`, or `gsub("AMP.","",dataframe$gene_name)`. …
Answer: Workshop for population genomics by pabe • 0
I highly recommend http://popgen.dk/popgen21/ They provide an annual summer course so keep an eye out for 2022. In the meantime, here a…
Comment: Whole genome coverage plot by ATpoint 54k
He says > No, do not align to masked genome for any purpose. Filter out the reads mapped to the masked region after whole-genome alignment…
Comment: Whole genome coverage plot by cmdcolin ★ 1.6k
i was skeptical of this but here is lh3 saying so also https://www.biostars.org/p/3232/#3235 :)
Comment: Workshop for population genomics by GenoMax 107k
There may be one in 2022. They seem to hold them every other year. This link is the for the last one: https://evomics.org/2020-workshop-on-…
Comment: Tools or Method for batch analysis of Paired end WES data in a queue way. by Jeremy Leipzig 20k
those tools definitely work in a breadth-first manner as you wanted
Answer: ROC_AUC curve for performance of a classification by Kevin Blighe 77k
> I want clarify on this point, is it possible to get AUC 100% It is possible but not credible. This can occur when the model is 'overfi…
Comment: IMPUTE2 -merge_ref_panels by Kevin Blighe 77k
If there are no warnings or errors, and the program indicates that the command was successful, then there should be output files with prefi…
Comment: ABOUT affymetrix genotyping console (GTC) software and TCGA CNV workflow by Kevin Blighe 77k
HI, if the copy number from GTC is 1, this equates to a log2 ratio of -1. Please see: log2(1 / 2) [1] -1 Why we use 2? - 2 is the…
Comment: bad file format in HMM file by pavelasquezv ▴ 20
It is true. Thanks a lot, Mensur. Now it is working well All the best Alex
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