Limit : all time
all time today this week this month this year
169 results • Page 1 of 4
Sort: Rank
Rank Views Votes Replies
Filtering for tag: parsing • reset
3
votes
5
replies
253
views
Fast parsing genbank files
Genbank parsing R
updated 3 days ago by 87k • written 5 days ago by ▴ 210
4
votes
8
replies
265
views
Extracting the Best sequence per genomic region in a genome based on the Best e-value
genome e-value parsing Forum
7 weeks ago by johnny.sf ▴ 10
0
votes
1
reply
167
views
SnpSift set intersection with EFF annotations
snpsift variant annotation parsing
3 months ago by Richard ▴ 580
2
votes
2
replies
3.9k
views
Clustalw Multiple Sequence Alignment Parsing
parsing
updated 4 months ago by 20 • written 10.9 years ago by ★ 3.3k
0
votes
0
replies
193
views
How to do parsing of HGVSp ids?
parsing HGVS HGVSp snp
5 months ago by salamonj9 • 0
0
votes
1
reply
914
views
Masking and Parsing problem in Standalone BLAST 2.7.1?
masking parsing blastdbcmd NCBI BLAST makeblastdb
updated 7 months ago by • 0 • written 2.8 years ago by ▴ 20
1
vote
6
replies
892
views
How to remove newline of a FASTA file?
FASTA Python Header Parsing
updated 10 months ago by 19k • written 10 months ago by • 0
0
votes
0
replies
959
views
Understanding minimap2 output (PAF format)
minimap2 PAF Parsing RNA-SEQ
10 months ago by Rogerio Ribeiro ▴ 50
0
votes
1
reply
194
views
conservative position extraction
sequence consensus conservative fastq parsing
updated 11 months ago by 12k • written 11 months ago by • 0
1
vote
1
reply
211
views
Get duplicate GO ids
parsing genbank biopython
13 months ago by iCosmoso • 0
0
votes
0
replies
353
views
News: UniProt: Functional annotation of different gene products in UniProtKB/Swiss-Prot
uniprot format xml parsing protein News
16 months ago by Elisabeth Gasteiger ★ 1.9k
3
votes
1
reply
535
views
News: UniProt: Change of FT and CC section in UniProtKB text format
uniprot parsing format protein News
16 months ago by Elisabeth Gasteiger ★ 1.9k
1
vote
0
replies
598
views
NCBI Taxon ID to IMG Genome IDs
bioinformatics parsing html parsing IDs
21 months ago by Mohak ▴ 10
2
votes
2
replies
1.9k
views
Pathview parsing error
pathview R parsing
updated 21 months ago by ★ 2.0k • written 3.4 years ago by ▴ 40
1
vote
5
replies
473
views
Parsing VCF Data
vcf parsing chromosome tag
updated 21 months ago by 32k • written 21 months ago by ▴ 10
9
votes
12
replies
676
views
Convert fasta headers to GFF
RNA-Seq gff parsing tophat HTseq
22 months ago by alexis.groppi ▴ 30
3
votes
5
replies
844
views
How can I parse a json file from MobiDB to retrieve proteome data?
database annotation parsing proteins format
updated 2.2 years ago by • 0 • written 2.3 years ago by • 0
3
votes
6
replies
1.1k
views
UniProtKB - mapping gene name to ID (*_HUMAN ) using python2
uniprot databases parsing python api
updated 2.3 years ago by ★ 2.5k • written 2.3 years ago by • 0
1
vote
1
reply
1.5k
views
Ensembl VEP cannot parse HGVS notation.
VEP HGVS REF_SEQ PARSING Ensembl
updated 2.6 years ago by 10k • written 4.9 years ago by ▴ 30
20
votes
5
replies
8.0k
views
Going From Cigar String In Sam To Genomic Coordinates?
sam parsing cigar alignment
updated 2.6 years ago by 32k • written 10.8 years ago by ▴ 810
19
votes
11
replies
8.0k
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 2.6 years ago by 32k • written 10.8 years ago by ▴ 30
4
votes
3
replies
5.9k
views
Efficient Fastq Parsing And Manipulation In Java (With Or Without Biojava)
fastq java biojava parsing
updated 2.6 years ago by 32k • written 10.8 years ago by 48k
14
votes
13
replies
3.6k
views
Parsing Custom Snp Info File In Python
python parsing file
updated 2.6 years ago by 32k • written 10.8 years ago by 11k
108
votes
28
replies
117k
views
15 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 2.6 years ago by 32k • written 11.0 years ago by 11k
0
votes
1
reply
576
views
Parsing online blast results using NCBIXML returns 50 alignments per Blast.Record object
python parsing biopython NCBIXML
2.7 years ago by aleksanderczeszyk • 0
7
votes
12
replies
11k
views
6 follow
Downloading Data From Mg-Rast
parsing
updated 2.8 years ago by ▴ 350 • written 7.1 years ago by ▴ 790
5
votes
6
replies
1.7k
views
Extracting Sub-cellular location from Uniprot into tabular format
SwissProt UniProt Parsing
updated 2.8 years ago by ★ 1.9k • written 2.8 years ago by 48k
3
votes
7
replies
1.2k
views
SAM CIGAR parsing and position counter in R
SAM CIGAR parsing R
2.9 years ago by niu.shengyong ▴ 60
3
votes
9
replies
1.0k
views
using awk to extract a specific pattern
gff extract awk parsing
3.0 years ago by Chvatil ▴ 60
4
votes
9
replies
4.4k
views
Problem parsing interval list file to GenomicsDBImport in GATK4
gatk interval parsing GVCF
updated 3.0 years ago by • 0 • written 3.3 years ago by ▴ 20
1
vote
10
replies
1.7k
views
How to parse a pubmed abstract that contains html tags or Unicode in python?
python xml pubmed parsing html
updated 3.0 years ago by 135k • written 3.0 years ago by • 0
0
votes
2
replies
812
views
RNA Structure prediction using context free grammar
structure prediction rna grammar parsing
3.0 years ago by maria.sedsvit • 0
6
votes
7
replies
2.3k
views
convert CSQ and ANN fields to a tab delimitet document with its headers
VCF CSQ ANN PARSING PERL
updated 3.2 years ago by 135k • written 3.2 years ago by ▴ 20
8
votes
6
replies
5.8k
views
Syntax For Neighborsearch Module In Biopython
biopython pdb parsing
updated 3.3 years ago by • 0 • written 10.7 years ago by ▴ 120
3
votes
5
replies
1.3k
views
Parsing fasta file using seqIO
sequence biopython Fasta parsing
updated 3.4 years ago by 19k • written 3.4 years ago by • 0
3
votes
9
replies
2.0k
views
parse nxml file from pubmed
nxml parsing pubmed
updated 3.5 years ago by 135k • written 3.5 years ago by ▴ 380
0
votes
2
replies
833
views
How I get mRNA accession no if I have gene name and location with the help of perl
mRNA miRNA Perl Parsing
updated 3.6 years ago by ▴ 470 • written 3.6 years ago by ▴ 30
3
votes
4
replies
1.1k
views
Trimming local GB file with Biopython
python biopython genbank parsing
updated 3.6 years ago by 19k • written 3.6 years ago by • 0
1
vote
2
replies
1.0k
views
From sam data, how do I tell from which fastq file each read came from?
sam parsing read file origin bowtie2
3.7 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 3.9 years ago by 20 • written 10.0 years ago by ▴ 20
2
votes
4
replies
1.0k
views
genome features and sequence parsing
genome sequence cds parsing
updated 4.0 years ago by ★ 3.4k • written 4.0 years ago by ★ 1.1k
5
votes
14
replies
2.5k
views
Help extracting the taxonomy for a file containing a list of accession numbers from Genbank
sequence gene taxonomy parsing
updated 4.1 years ago by ▴ 10 • written 5.1 years ago by ▴ 50
8
votes
11
replies
2.4k
views
6 follow
Parsing FASTA file using class in Python
Python Biopython Class Parsing FASTA
updated 4.1 years ago by 9.5k • written 4.1 years ago by ▴ 30
20
votes
23
replies
4.2k
views
11 follow
Parse Fastq File - Pad Reads With N'S
fastq parsing
updated 4.1 years ago by ▴ 50 • written 9.2 years ago by ▴ 570
2
votes
4
replies
1.3k
views
parsing tabular blast output
parsing tabular blast
updated 4.1 years ago by 135k • written 4.1 years ago by • 0
3
votes
13
replies
1.5k
views
parsing only 100% identical hits out of BLAST tab
blast tabular parsing
updated 4.1 years ago by 20 • written 4.2 years ago by 19k
4
votes
4
replies
1.7k
views
NCBI: Parsing data nicely?
parsing data table ncbi geo
updated 4.2 years ago by 9.7k • written 4.2 years ago by ▴ 30
3
votes
4
replies
3.0k
views
parsing cd-hit result
cd-hit parsing
updated 4.3 years ago by ★ 2.9k • written 4.3 years ago by ▴ 210
0
votes
11
replies
952
views
chrY.fa parsing problem
SNP parsing fasta
4.3 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 4.5 years ago by ▴ 280 • written 10.2 years ago by ▴ 40
169 results • Page 1 of 4
Recent Votes
ELIXIR Training Coordinator (pan-European bioinformatics training)
Answer: What Do You Waste Your Time On
Answer: Samtools sort: too many open files error
Is it bad practice to change threshold for interaction probability?
Answer: Is it bad practice to change threshold for interaction probability?
What to put in my Github
Comment: What to put in my Github
Recent Locations • All
United Kingdom, just now
Novosibirsk, just now
Netherlands, just now
Norway, 2 minutes ago
India/Ahmedabad, 2 minutes ago
United Kingdom, 2 minutes ago
Spain, 3 minutes ago
Recent Awards • All
Popular Question to lakhujanivijay 5.4k
Appreciated to William ★ 4.8k
Scholar to Bastien Hervé 4.9k
Popular Question to Thomas ▴ 100
Popular Question to rekren ▴ 30
Teacher to Michael Dondrup 48k
Popular Question to Sej Modha 4.8k
Recent Replies
Comment: Converting Braker2 gtf output to gff then genbank by Juke34 ★ 5.3k
You can get some information calling the EMBLmyGFF3 adanced help: ``` EMBLmyGFF3 --advanced_help topology ``` Otherwise you can find verbo…
Comment: Converting Braker2 gtf output to gff then genbank by robert.murphy ▴ 40
In `EMBLmyGFF3` script should I concern myself much with the `topology` option? If yes do you have suggestions for good places to educate (…
Comment: Why GC content is important on NIPT results? by German.M.Demidov ★ 2.0k
NIIPT can be performed in various variations and for different purposes. Is it chromosome abnormalities test in your case? If so, extreme G…
Comment: bedops wig2bed 'Row begins with a tab or space' error by a_bis • 0
The output looks as follows: 1^I0^I3000060^I0.000000$ 1^I3000060^I3000090^I0.224911$ 1^I3000090^I3000120^I0.449820$ 1^I30…
Comment: Samtools view filter by reference sequence by maxrwjones898 • 0
Thanks for your answer, I will give this a go!
Answer: Variant calling from comparison of assembled genomes where there is only one r by Hans ▴ 120
It appears that bcftools takes into consideration the alignments of all genotypes when it calls variants. When I call the variants separat…
Comment: What Coverage allele-fraction threshold to use? by German.M.Demidov ★ 2.0k
At each genomic position you have a specific coverage, say X. Y out of X reads may support an alternative variant, X - Y - reference. You n…
Answer: Finding all instances of a recurring motif in a repeat protein by Mensur Dlakic ★ 10k
Some papers to consider: - https://academic.oup.com/bioinformatics/article/24/6/807/194276 - https://academic.oup.com/bib/article/15/…
Comment: why my volcano plot looks strange? by ATpoint 47k
First thing to do would be to not use custom statistics but a proper framework such as limma. There are quite some peptides (or whatever yo…
Answer: Help with CNV calling using ExomeDepth by Joakim ▴ 10
Instead of using bedframes from data(genes.hg19) and data(exons.hg19) in ExomeDepth, I got them from the UCSC Table Browser for hg38 (http:…
Answer: How to grep scaffold from the vcf file by Pierre Lindenbaum 135k
bcftools view --regions-file file1.txt input.vcf
Comment: How Can I Merge A Large Amount Of Vcf Files? by Thind amarinder ▴ 130
how to add, one more column with for sample names (e.g base name of the file) Tried the following it worked sed 's/$/\t'"$input"'/' $inp…
Comment: vcftools intersect vs bedtools intersect by Alex Reynolds 32k
`--intersect` means something different in `bedops` than it does in other tools. With `--element-of`, this is a set membership test: does t…
Answer: For loop - mkdir and command by 5heikki 9.6k
Perhaps: for F in *.fasta; do mkdir /Users/laura/bio/insilicoseq/$(basename "$F" .fasta) iss generate \ -…
Comment: why my volcano plot looks strange? by hellocita ▴ 30
Thanks for your help! Now it looks better, and there are still many dots near the middle line, was this acceptable?
Traffic: 2560 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6