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Showing top results for tag: parsing • reset
3
votes
5
replies
518
views
Fast parsing genbank files
Genbank parsing R
updated 3 months ago by 88k • written 3 months ago by ▴ 210
4
votes
8
replies
347
views
Extracting the Best sequence per genomic region in a genome based on the Best e-value
genome e-value parsing Forum
5 months ago by johnny.sf ▴ 20
0
votes
1
reply
285
views
SnpSift set intersection with EFF annotations
snpsift variant annotation parsing
7 months ago by Richard ▴ 580
2
votes
2
replies
4.0k
views
Clustalw Multiple Sequence Alignment Parsing
parsing
updated 7 months ago by 20 • written 11.2 years ago by ★ 3.3k
0
votes
0
replies
283
views
How to do parsing of HGVSp ids?
parsing HGVS HGVSp snp
8 months ago by salamonj9 • 0
0
votes
1
reply
981
views
Masking and Parsing problem in Standalone BLAST 2.7.1?
masking parsing blastdbcmd NCBI BLAST makeblastdb
updated 11 months ago by • 0 • written 3.1 years ago by ▴ 20
1
vote
6
replies
1.1k
views
How to remove newline of a FASTA file?
FASTA Python Header Parsing
updated 13 months ago by 19k • written 13 months ago by • 0
0
votes
0
replies
1.3k
views
Understanding minimap2 output (PAF format)
minimap2 PAF Parsing RNA-SEQ
13 months ago by Rogerio Ribeiro ▴ 50
0
votes
1
reply
239
views
conservative position extraction
sequence consensus conservative fastq parsing
updated 14 months ago by 12k • written 14 months ago by • 0
1
vote
1
reply
251
views
Get duplicate GO ids
parsing genbank biopython
17 months ago by iCosmoso • 0
0
votes
0
replies
405
views
News: UniProt: Functional annotation of different gene products in UniProtKB/Swiss-Prot
uniprot format xml parsing protein News
19 months ago by Elisabeth Gasteiger ★ 1.9k
3
votes
1
reply
599
views
News: UniProt: Change of FT and CC section in UniProtKB text format
uniprot parsing format protein News
19 months ago by Elisabeth Gasteiger ★ 1.9k
1
vote
0
replies
727
views
NCBI Taxon ID to IMG Genome IDs
bioinformatics parsing html parsing IDs
2.0 years ago by Mohak ▴ 10
2
votes
2
replies
2.0k
views
Pathview parsing error
pathview R parsing
updated 2.0 years ago by ★ 2.0k • written 3.7 years ago by ▴ 40
1
vote
5
replies
546
views
Parsing VCF Data
vcf parsing chromosome tag
updated 2.1 years ago by 34k • written 2.1 years ago by ▴ 10
9
votes
12
replies
803
views
Convert fasta headers to GFF
RNA-Seq gff parsing tophat HTseq
2.1 years ago by alexis.groppi ▴ 30
3
votes
5
replies
919
views
How can I parse a json file from MobiDB to retrieve proteome data?
database annotation parsing proteins format
updated 2.4 years ago by • 0 • written 2.5 years ago by • 0
3
votes
6
replies
1.2k
views
UniProtKB - mapping gene name to ID (*_HUMAN ) using python2
uniprot databases parsing python api
updated 2.6 years ago by ★ 2.6k • written 2.6 years ago by • 0
1
vote
1
reply
1.6k
views
Ensembl VEP cannot parse HGVS notation.
VEP HGVS REF_SEQ PARSING Ensembl
updated 2.8 years ago by 10k • written 5.2 years ago by ▴ 30
20
votes
5
replies
8.2k
views
Going From Cigar String In Sam To Genomic Coordinates?
sam parsing cigar alignment
updated 2.9 years ago by 34k • written 11.0 years ago by ▴ 810
19
votes
11
replies
8.2k
views
8 follow
How To Extract Just The Coordinate Values From A Pdb File Converted To A Text File, In Java Only?
coordinates java pdb parsing structure
updated 2.9 years ago by 34k • written 11.1 years ago by ▴ 30
4
votes
3
replies
6.1k
views
Efficient Fastq Parsing And Manipulation In Java (With Or Without Biojava)
fastq java biojava parsing
updated 2.9 years ago by 34k • written 11.1 years ago by 49k
14
votes
13
replies
3.7k
views
Parsing Custom Snp Info File In Python
python parsing file
updated 2.9 years ago by 34k • written 11.1 years ago by 11k
109
votes
28
replies
123k
views
15 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 2.9 years ago by 34k • written 11.3 years ago by 11k
0
votes
1
reply
642
views
Parsing online blast results using NCBIXML returns 50 alignments per Blast.Record object
python parsing biopython NCBIXML
3.0 years ago by aleksanderczeszyk • 0
7
votes
12
replies
12k
views
6 follow
Downloading Data From Mg-Rast
parsing
updated 3.1 years ago by ▴ 350 • written 7.4 years ago by ▴ 800
5
votes
6
replies
1.9k
views
Extracting Sub-cellular location from Uniprot into tabular format
SwissProt UniProt Parsing
updated 3.1 years ago by ★ 1.9k • written 3.1 years ago by 49k
3
votes
7
replies
1.3k
views
SAM CIGAR parsing and position counter in R
SAM CIGAR parsing R
3.2 years ago by niu.shengyong ▴ 70
3
votes
9
replies
1.1k
views
using awk to extract a specific pattern
gff extract awk parsing
3.3 years ago by Chvatil ▴ 60
4
votes
9
replies
4.7k
views
Problem parsing interval list file to GenomicsDBImport in GATK4
gatk interval parsing GVCF
updated 3.3 years ago by • 0 • written 3.6 years ago by ▴ 20
1
vote
10
replies
1.9k
views
How to parse a pubmed abstract that contains html tags or Unicode in python?
python xml pubmed parsing html
updated 3.3 years ago by 137k • written 3.3 years ago by • 0
0
votes
2
replies
865
views
RNA Structure prediction using context free grammar
structure prediction rna grammar parsing
3.3 years ago by maria.sedsvit • 0
6
votes
7
replies
2.5k
views
convert CSQ and ANN fields to a tab delimitet document with its headers
VCF CSQ ANN PARSING PERL
updated 3.5 years ago by 137k • written 3.5 years ago by ▴ 20
8
votes
6
replies
5.9k
views
Syntax For Neighborsearch Module In Biopython
biopython pdb parsing
updated 3.6 years ago by • 0 • written 11.0 years ago by ▴ 120
3
votes
5
replies
1.5k
views
Parsing fasta file using seqIO
sequence biopython Fasta parsing
updated 3.7 years ago by 19k • written 3.7 years ago by • 0
3
votes
9
replies
2.2k
views
parse nxml file from pubmed
nxml parsing pubmed
updated 3.8 years ago by 137k • written 3.8 years ago by ▴ 380
0
votes
2
replies
889
views
How I get mRNA accession no if I have gene name and location with the help of perl
mRNA miRNA Perl Parsing
updated 3.8 years ago by ▴ 470 • written 3.8 years ago by ▴ 40
3
votes
4
replies
1.1k
views
Trimming local GB file with Biopython
python biopython genbank parsing
updated 3.8 years ago by 19k • written 3.8 years ago by • 0
1
vote
2
replies
1.1k
views
From sam data, how do I tell from which fastq file each read came from?
sam parsing read file origin bowtie2
4.0 years ago by bitjunkie ▴ 40
21
votes
19
replies
14k
views
8 follow
How To Extract Just The Coordinate Values From A Pdb File, Using Perl Only?
pdb protein coordinates parsing perl
updated 4.2 years ago by 20 • written 10.3 years ago by ▴ 20
2
votes
4
replies
1.1k
views
genome features and sequence parsing
genome sequence cds parsing
updated 4.3 years ago by ★ 3.4k • written 4.3 years ago by ★ 1.1k
5
votes
14
replies
2.6k
views
Help extracting the taxonomy for a file containing a list of accession numbers from Genbank
sequence gene taxonomy parsing
updated 4.3 years ago by ▴ 10 • written 5.4 years ago by ▴ 50
8
votes
11
replies
2.5k
views
6 follow
Parsing FASTA file using class in Python
Python Biopython Class Parsing FASTA
updated 4.4 years ago by 9.6k • written 4.4 years ago by ▴ 30
20
votes
23
replies
4.3k
views
11 follow
Parse Fastq File - Pad Reads With N'S
fastq parsing
updated 4.4 years ago by ▴ 50 • written 9.5 years ago by ▴ 570
2
votes
4
replies
1.3k
views
parsing tabular blast output
parsing tabular blast
updated 4.4 years ago by 137k • written 4.4 years ago by • 0
3
votes
13
replies
1.6k
views
parsing only 100% identical hits out of BLAST tab
blast tabular parsing
updated 4.4 years ago by 20 • written 4.5 years ago by 19k
4
votes
4
replies
1.8k
views
NCBI: Parsing data nicely?
parsing data table ncbi geo
updated 4.5 years ago by 9.7k • written 4.5 years ago by ▴ 30
3
votes
4
replies
3.2k
views
parsing cd-hit result
cd-hit parsing
updated 4.6 years ago by ★ 2.9k • written 4.6 years ago by ▴ 220
0
votes
11
replies
1.0k
views
chrY.fa parsing problem
SNP parsing fasta
4.6 years ago by michael • 0
10
votes
2
replies
12k
views
Illumina'S Genome Studio Final Report: Forward Or Top Allele?
allele snp illumina parsing
updated 4.7 years ago by ▴ 290 • written 10.5 years ago by ▴ 40
50 results • Page 1 of 1
Recent Votes
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
How to generate a .sam/.bam file of a particular chromosome or even a particular region?
How To Split A Bam File By Chromosome
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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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