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Showing top results for tag: script • reset
0
votes
0
replies
68
views
Use grep to loop a command in a script
snps grep vcftools script bash
updated 1 day ago by 106k • written 1 day ago by • 0
1
vote
2
replies
222
views
R script for offspring GO terms
multiple script terms GO
5 weeks ago by margot.27.muller • 0
4
votes
6
replies
381
views
HT-Seq Batch
Batch script HT-Seq
updated 11 weeks ago by ★ 1.1k • written 11 weeks ago by • 0
0
votes
2
replies
170
views
Script for cascade molecular dynamics
cascading script moleculardynamics
11 weeks ago by Samilla • 0
3
votes
4
replies
294
views
How to create boxplot with jitter points where one point is labelled
Boxplot script Labell Jitter R
3 months ago by Roland • 0
1
vote
6
replies
737
views
syntax error near unexpected token `('
script shell
updated 3 months ago by 34k • written 3 months ago by • 0
6
votes
6
replies
417
views
Trimming an alignment around a given sequence
pairwise script crop alignment
4 months ago by QLFblaireau ▴ 30
2
votes
21
replies
1.5k
views
How to loop on two fasta files for hetero-dimerization analysis
fasta script python sequence
updated 5 months ago by 17k • written 5 months ago by ▴ 50
0
votes
2
replies
311
views
IF statement (in linux script) to merge Fastq files with similar (but not the same) names
unix script ifstatement linux fastq
updated 5 months ago by 17k • written 5 months ago by ▴ 30
0
votes
0
replies
191
views
How can I extract information from tRNA encoding genes only (Python)?
Python gc3 script
6 months ago by amirah.rafique • 0
0
votes
5
replies
279
views
About shell script
script alignment
updated 7 months ago by 10k • written 7 months ago by ▴ 10
2
votes
6
replies
406
views
Blast + Alignement Shell Script
alignment script blast shell Tutorial
updated 8 months ago by ▴ 270 • written 8 months ago by • 0
2
votes
6
replies
510
views
problem use htseq-count in bash script
htseq-count script
10 months ago by o.omidan ▴ 10
1
vote
4
replies
253
views
how can I write a script for calculate snp variants coverage
script bash genomecoverage variantcoverage
10 months ago by tacidilceren • 0
0
votes
5
replies
1.3k
views
Calculate numbers of indels <=2 nt within sam
script
updated 10 months ago by 20 • written 4.3 years ago by ★ 1.3k
0
votes
6
replies
1.6k
views
Split one embl file into several
script python perl
updated 12 months ago by 20 • written 6.3 years ago by • 0
6
votes
4
replies
582
views
Script to obtain human protein sequences by the gene symbols
script gene protein
updated 14 months ago by ▴ 150 • written 15 months ago by ★ 8.8k
11
votes
10
replies
4.6k
views
Errors In A Bioperl Script, Please Help Me To Have A Check, Thanks In Advance!
bioperl script blast
updated 14 months ago by 20 • written 8.3 years ago by ▴ 40
3
votes
3
replies
340
views
Error python script overlapping_reads.py
python script github
16 months ago by Amaranta Remedios ▴ 10
0
votes
2
replies
302
views
BLAST and GFF script to find locations of SNPs
BLAST gff script SNP
16 months ago by Kiki_01 • 0
4
votes
7
replies
493
views
bash bowtie script output with prefix
bash script unix
updated 16 months ago by 19k • written 16 months ago by ▴ 10
2
votes
4
replies
879
views
Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
hmm hmmer protein domain bash script
updated 17 months ago by ★ 13k • written 17 months ago by ▴ 370
0
votes
0
replies
439
views
HMMSCAN error in batch submission
bash HMM script
19 months ago by geizetomazetto • 0
1
vote
2
replies
770
views
Prokka Python Script for Gene Annotation
Python Prokka Script Annotation Linux
updated 21 months ago by ★ 13k • written 21 months ago by ▴ 40
3
votes
3
replies
431
views
Python to R
python R CODE Script Convert
written 21 months ago by • 0
2
votes
4
replies
511
views
Results of two sequential bash pipes into a variable instead of a file?
bash pipe variable shell script
updated 21 months ago by 20 • written 24 months ago by • 0
3
votes
8
replies
469
views
Converting amino acid sequences to numerical values
R perl python sequence script
updated 22 months ago by 12k • written 23 months ago by ▴ 10
2
votes
5
replies
514
views
Merge overlapping intervals in a bed file containing different chromosomes
merge bed script
updated 24 months ago by 138k • written 24 months ago by ▴ 30
1
vote
2
replies
415
views
Help with Python script
python script
updated 2.0 years ago by 106k • written 2.0 years ago by ▴ 10
0
votes
3
replies
370
views
Inserting bash and bioinformatic's scripts into browser database
browser script bash java python
2.0 years ago by flogin ▴ 270
9
votes
9
replies
2.4k
views
Perl loop woes
script perl for loop ortho groups phylogentics
updated 2.2 years ago by 20 • written 3.3 years ago by • 0
1
vote
7
replies
779
views
intersection for several file
RNA-Seq sequencing script
updated 2.3 years ago by ★ 1.3k • written 2.3 years ago by ▴ 40
9
votes
13
replies
1.6k
views
Python Script to map reads to reference sequence
sequence python mapping script reference sequence
2.4 years ago by Fid_o ▴ 40
4
votes
6
replies
3.2k
views
Create a plot based on binary input of 1s and 0s.
R script plot
updated 2.4 years ago by 10k • written 2.4 years ago by ▴ 210
2
votes
4
replies
582
views
Is it possible to print DNA sequences of subject organism in tblastn?
BLAST alignment tblastn sequence analysis script
2.5 years ago by Kumar ▴ 50
4
votes
2
replies
713
views
Help with iTol annotation python script
python itol script
updated 2.5 years ago by ★ 2.6k • written 2.5 years ago by • 0
4
votes
5
replies
883
views
Blast script over multiple databases
blastn script multipledatabases
2.5 years ago by dllopezr ▴ 80
5
votes
4
replies
593
views
Writing scripts for a single vs all chromosomes
RNA-Seq script shell
2.5 years ago by Antonio.Aubry ▴ 10
0
votes
2
replies
818
views
Read In Function for BAM file processing
Script BAM
2.5 years ago by Jonas.Koch • 0
11
votes
18
replies
1.4k
views
6 follow
How to extract filename and change text in the same file
sequence VCF Script
updated 2.6 years ago by ★ 1.3k • written 2.6 years ago by ▴ 210
1
vote
2
replies
2.4k
views
Bash script iterating over 2 arrays
bash script loops multiple arrays
2.6 years ago by mdriskil ▴ 10
2
votes
3
replies
702
views
Bash and seqret problem
bash seqret script
2.6 years ago by MichaelTrev ▴ 10
0
votes
1
reply
1.4k
views
Problem installing GATK
GATK script software error Ubuntu
updated 2.6 years ago by 14k • written 2.6 years ago by • 0
8
votes
7
replies
9.6k
views
TrimGalore! on multiple paired fastq files
rna-seq trimgalore! paired-end script
updated 2.6 years ago by ▴ 10 • written 4.9 years ago by ▴ 60
0
votes
8
replies
996
views
how to change the sequence ID and order of sequences in a file to match an alignment output file
python script
updated 2.7 years ago by 6.1k • written 2.7 years ago by ▴ 10
0
votes
10
replies
939
views
How to add name of genus and species automatically in headers of a multi-FASTA file after run BLASTn?
BLASTN RENAME HEADER MULTI-FASTA SCRIPT
updated 2.7 years ago by 20 • written 2.9 years ago by • 0
2
votes
4
replies
841
views
How to change the path so that screen can take the default python path?
python script issue
updated 2.8 years ago by ★ 1.2k • written 2.8 years ago by ▴ 80
3
votes
2
replies
675
views
Python script strange behavior
python script
3.0 years ago by dllopezr ▴ 80
8
votes
13
replies
1.3k
views
Editing fasta headers with bash
fasta headers fasta bash script
updated 3.0 years ago by 19k • written 3.0 years ago by ▴ 20
17
votes
10
replies
3.2k
views
6 follow
Extract only rows with main chromosomes (1-22, X, Y) on first column?
linux grep R script
updated 3.1 years ago by ★ 2.5k • written 3.1 years ago by ▴ 280
50 results • Page 1 of 1
Recent Votes
Comment: TCGA dataset normalization
Understanding Imputed Genotypes
C: Cox regression survival analysis - using a panel of genes with TCGA
C: Scaling data using Pheatmap
C: Scaling data using Pheatmap
A: Database of HERV integration locations
A: Database of HERV integration locations
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Recent Replies
Comment: RIP-seq : normalize Input with Immunoprecipitated raw counts or not by ATpoint 53k
I have no experience with RIP-seq but usually in something like ChIP-seq one only uses inputs for peak calling as they are globally differe…
Comment: Quick questions about Alevin and AlevinQC by ATpoint 53k
> When I run AlevinQC why the Number of used reads (which Alevin documentation says are reads that are used for quantification) greater tha…
Comment: Problem with viewing BAM files in IGV by Pierre Lindenbaum 138k
> as verified by inspecting the BAM file with samtools view show us a few lines of "samtools view" and show us the screenshot of IGV for …
Answer: compare two vcf files by 순연 • 0
thank u sir , happy Korean Thanksgiving Day 1) how you want to rank those common rs IDs 선생님이 알려주신 코드를 이용해서 두개의 파일에 중복되는 rsID가 있고 또한 여…
Comment: Doing multiple testing correction before or after GO analysis by dsull ★ 2.3k
Honestly speaking, your gene list is not "statistically robust" (it's arbitrary since you have no sense of the actual false discovery rate)…
Comment: bedtools getfasta concatenating sequences by Juke34 ★ 6.3k
Ok it is because the first command create gene features only and the second remove gene feature if they do not have any sub-feature like mR…
Comment: What does it mean BLASTx in de novo RNAseq analysis? by lieven.sterck 12k
yes, that is very possible indeed. however, running blastx on the 'raw' genomic is somewhat less intuitive to interpret. If you have annot…
Comment: TPM value from DESE2 and significant filterig isssue by ATpoint 53k
Hi, could you please reformat this post using the code `10101` option to highlight code and data?
Comment: desEQ2 eRROR by Nai • 0
res_ddsDE_new has 36,000 rows. When I am using subset(res_ddsDE_new, padj < 0.05 & abs(log2FoldChange) > 1) res_ddsDE_new baseMean log2Fo…
Comment: TCGA dataset normalization by ruby4bioinfo • 0
Thanks Kevin, i got following output str(countData) 'data.frame': 60488 obs. of 183 variables: $ Ensembl_ID : chr "ENSG00000000003…
Comment: Why there are same name with different value in my microarray result? by Aki • 0
Thank you JC! Do you know how to combine these spots as one miRNA? Or do we treat them differently?
Comment: What does it mean BLASTx in de novo RNAseq analysis? by Riku ▴ 40
Thank you very much for your advices! I see. It's an indicator of the quality of the assembly. Can this be done by running BLAST on the f…
Comment: DE analysis using technical replicates by vineshkamble23 • 0
Okay Thank you so much for the explanation
Comment: TCGA dataset normalization by dsull ★ 2.3k
Because FPKMs are terrible for between-samples normalization; furthermore, the GDC website's pipeline is a bit dated (xena uses kallisto an…
Answer: Trouble running vcf2bam jvarkit tool by Ayush • 0
hello guys i am just trying to convert vcf file to bam file how did you use that VCF2BAM jvarkit can you show me example
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