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Showing top results for tag: parsing • reset
1
vote
2
replies
245
views
Parsing issues with single cell file from GEO
cell single parsing R
updated 8 weeks ago by 77k • written 8 weeks ago by • 0
18
votes
15
replies
16k
views
9 follow
Tools Parsing Ncbi Blast -M 7 Xml Output Format?
blast xml parsing
updated 8 weeks ago by • 0 • written 10.5 years ago by ▴ 730
3
votes
5
replies
592
views
Fast parsing genbank files
Genbank parsing R
updated 5 months ago by 89k • written 5 months ago by ▴ 220
4
votes
8
replies
393
views
Extracting the Best sequence per genomic region in a genome based on the Best e-value
genome e-value parsing Forum
7 months ago by johnny.sf ▴ 20
0
votes
1
reply
390
views
SnpSift set intersection with EFF annotations
snpsift variant annotation parsing
9 months ago by Richard ▴ 580
2
votes
2
replies
4.1k
views
Clustalw Multiple Sequence Alignment Parsing
parsing
updated 9 months ago by 20 • written 11.4 years ago by ★ 3.3k
0
votes
0
replies
374
views
How to do parsing of HGVSp ids?
parsing HGVS HGVSp snp
11 months ago by salamonj9 • 0
0
votes
1
reply
1.0k
views
Masking and Parsing problem in Standalone BLAST 2.7.1?
masking parsing blastdbcmd NCBI BLAST makeblastdb
updated 13 months ago by • 0 • written 3.2 years ago by ▴ 20
1
vote
6
replies
1.3k
views
How to remove newline of a FASTA file?
FASTA Python Header Parsing
updated 15 months ago by 19k • written 15 months ago by • 0
0
votes
0
replies
1.5k
views
Understanding minimap2 output (PAF format)
minimap2 PAF Parsing RNA-SEQ
15 months ago by Rogerio Ribeiro ▴ 60
0
votes
1
reply
272
views
conservative position extraction
sequence consensus conservative fastq parsing
updated 16 months ago by 12k • written 16 months ago by • 0
1
vote
1
reply
276
views
Get duplicate GO ids
parsing genbank biopython
19 months ago by iCosmoso • 0
0
votes
0
replies
435
views
News: UniProt: Functional annotation of different gene products in UniProtKB/Swiss-Prot
uniprot format xml parsing protein News
21 months ago by Elisabeth Gasteiger ★ 1.9k
3
votes
1
reply
643
views
News: UniProt: Change of FT and CC section in UniProtKB text format
uniprot parsing format protein News
21 months ago by Elisabeth Gasteiger ★ 1.9k
1
vote
0
replies
819
views
NCBI Taxon ID to IMG Genome IDs
bioinformatics parsing html parsing IDs
2.2 years ago by Mohak ▴ 10
2
votes
2
replies
2.2k
views
Pathview parsing error
pathview R parsing
updated 2.2 years ago by ★ 2.0k • written 3.9 years ago by ▴ 40
1
vote
5
replies
585
views
Parsing VCF Data
vcf parsing chromosome tag
updated 2.2 years ago by 34k • written 2.2 years ago by ▴ 10
9
votes
12
replies
881
views
Convert fasta headers to GFF
RNA-Seq gff parsing tophat HTseq
2.3 years ago by alexis.groppi ▴ 30
3
votes
5
replies
967
views
How can I parse a json file from MobiDB to retrieve proteome data?
database annotation parsing proteins format
updated 2.6 years ago by • 0 • written 2.7 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 2.8 years ago by ★ 2.7k • written 2.8 years ago by • 0
1
vote
1
reply
1.7k
views
Ensembl VEP cannot parse HGVS notation.
VEP HGVS REF_SEQ PARSING Ensembl
updated 3.0 years ago by 10k • written 5.3 years ago by ▴ 30
20
votes
5
replies
8.3k
views
Going From Cigar String In Sam To Genomic Coordinates?
sam parsing cigar alignment
updated 3.0 years ago by 34k • written 11.2 years ago by ▴ 820
19
votes
11
replies
8.3k
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 3.0 years ago by 34k • written 11.2 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 3.0 years ago by 34k • written 11.2 years ago by 49k
14
votes
13
replies
3.8k
views
Parsing Custom Snp Info File In Python
python parsing file
updated 3.0 years ago by 34k • written 11.3 years ago by 11k
112
votes
28
replies
127k
views
15 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 3.1 years ago by 34k • written 11.5 years ago by 11k
0
votes
1
reply
689
views
Parsing online blast results using NCBIXML returns 50 alignments per Blast.Record object
python parsing biopython NCBIXML
3.2 years ago by aleksanderczeszyk • 0
7
votes
12
replies
12k
views
6 follow
Downloading Data From Mg-Rast
parsing
updated 3.2 years ago by ▴ 360 • written 7.6 years ago by ▴ 800
5
votes
6
replies
2.0k
views
Extracting Sub-cellular location from Uniprot into tabular format
SwissProt UniProt Parsing
updated 3.2 years ago by ★ 1.9k • written 3.3 years ago by 49k
3
votes
7
replies
1.4k
views
SAM CIGAR parsing and position counter in R
SAM CIGAR parsing R
3.4 years ago by niu.shengyong ▴ 70
3
votes
9
replies
1.2k
views
using awk to extract a specific pattern
gff extract awk parsing
3.4 years ago by Chvatil ▴ 60
4
votes
9
replies
4.8k
views
Problem parsing interval list file to GenomicsDBImport in GATK4
gatk interval parsing GVCF
updated 3.4 years ago by • 0 • written 3.8 years ago by ▴ 20
1
vote
10
replies
2.1k
views
How to parse a pubmed abstract that contains html tags or Unicode in python?
python xml pubmed parsing html
updated 3.5 years ago by 138k • written 3.5 years ago by • 0
0
votes
2
replies
894
views
RNA Structure prediction using context free grammar
structure prediction rna grammar parsing
3.5 years ago by maria.sedsvit • 0
6
votes
7
replies
2.7k
views
convert CSQ and ANN fields to a tab delimitet document with its headers
VCF CSQ ANN PARSING PERL
updated 3.7 years ago by 138k • written 3.7 years ago by ▴ 20
8
votes
6
replies
6.0k
views
Syntax For Neighborsearch Module In Biopython
biopython pdb parsing
updated 3.7 years ago by • 0 • written 11.2 years ago by ▴ 120
3
votes
5
replies
1.6k
views
Parsing fasta file using seqIO
sequence biopython Fasta parsing
updated 3.9 years ago by 19k • written 3.9 years ago by • 0
3
votes
9
replies
2.3k
views
parse nxml file from pubmed
nxml parsing pubmed
updated 3.9 years ago by 138k • written 3.9 years ago by ▴ 380
0
votes
2
replies
918
views
How I get mRNA accession no if I have gene name and location with the help of perl
mRNA miRNA Perl Parsing
updated 4.0 years ago by ▴ 470 • written 4.0 years ago by ▴ 40
3
votes
4
replies
1.2k
views
Trimming local GB file with Biopython
python biopython genbank parsing
updated 4.0 years ago by 19k • written 4.0 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
4.2 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 4.4 years ago by 20 • written 10.5 years ago by ▴ 20
2
votes
4
replies
1.1k
views
genome features and sequence parsing
genome sequence cds parsing
updated 4.4 years ago by ★ 3.4k • written 4.4 years ago by ★ 1.1k
5
votes
14
replies
2.7k
views
Help extracting the taxonomy for a file containing a list of accession numbers from Genbank
sequence gene taxonomy parsing
updated 4.5 years ago by ▴ 10 • written 5.6 years ago by ▴ 60
8
votes
11
replies
2.6k
views
6 follow
Parsing FASTA file using class in Python
Python Biopython Class Parsing FASTA
updated 4.6 years ago by 9.7k • written 4.6 years ago by ▴ 30
20
votes
23
replies
4.4k
views
11 follow
Parse Fastq File - Pad Reads With N'S
fastq parsing
updated 4.6 years ago by ▴ 60 • written 9.6 years ago by ▴ 570
2
votes
4
replies
1.4k
views
parsing tabular blast output
parsing tabular blast
updated 4.6 years ago by 138k • written 4.6 years ago by • 0
3
votes
13
replies
1.6k
views
parsing only 100% identical hits out of BLAST tab
blast tabular parsing
updated 4.6 years ago by 20 • written 4.7 years ago by 19k
4
votes
4
replies
1.8k
views
NCBI: Parsing data nicely?
parsing data table ncbi geo
updated 4.7 years ago by 9.9k • written 4.7 years ago by ▴ 30
3
votes
4
replies
3.4k
views
parsing cd-hit result
cd-hit parsing
updated 4.8 years ago by ★ 2.9k • written 4.8 years ago by ▴ 220
50 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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