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Showing top results for tag:
Scripting
•
reset
281
votes
54
replies
10k
views
39 follow
Forum:
What Do You Waste Your Time On
bioinformatics
scripting
Forum
updated 4 days ago by
ponganta
▴ 170 • written 7.9 years ago by
Asaf
8.6k
40
votes
24
replies
805
views
13 follow
Forum:
What programming language do you use the most in your work? Which one do you like the best?
R
Python
Programming
Scripting
Forum
updated 9 weeks ago by
5heikki
9.7k • written 9 weeks ago by
DataStoryTeller
▴ 30
3
votes
0
replies
196
views
News:
Online training - Unix and shell scripting for bioinformatics
Unix
Bioinformatics
scripting
Linux
News
11 weeks ago by
carlopecoraro2
★ 2.0k
0
votes
4
replies
199
views
error when running NGS tools in bash script
software error
automation
scripting
3 months ago by
bertb
▴ 10
5
votes
8
replies
484
views
Remove duplicates from fasta keeping at least one sequence per group based on header
scripting
fasta
8 months ago by
vixelaa
▴ 20
11
votes
15
replies
671
views
Cutadapt for loop issue
unix
cutadapt
scripting
forloop
updated 12 months ago by
GouthamAtla
11k • written 12 months ago by
geneart$$
▴ 40
0
votes
0
replies
581
views
Job:
Senior Bioinformatician / Developer (Genome Annotation), Earlham Institute, Norwich, UK (5 days left to apply)
python
job
scripting
pipelines
genome annotation
Job
19 months ago by
cschu181
★ 2.6k
9
votes
10
replies
8.1k
views
Memory-Efficient Way To Transpose Csv/Text File?
matrix
scripting
updated 23 months ago by
Biostar
20 • written 7.5 years ago by
Click downvote
▴ 690
5
votes
2
replies
1.4k
views
How to merge/combine multiple vcf from different samples to make one multi sample vcf file using GATK
GATK
loop
scripting
updated 2.2 years ago by
Pierre Lindenbaum
135k • written 2.2 years ago by
S AR
▴ 60
4
votes
6
replies
530
views
Script for changing genes nomenclature
scripting
RNA-Seq
bedtools
updated 2.3 years ago by
vkkodali
★ 2.5k • written 2.3 years ago by
Francisco Muñoz
▴ 10
149
votes
44
replies
22k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
2.5 years ago by
Carlos Borroto
★ 1.9k
2
votes
1
reply
785
views
Job:
Bio/Informatician, Unit for Hematological Diagnostics, at the famous port city of Kiel, northern Germany
scripting
R
immunity
Job
updated 2.6 years ago by
Ram
32k • written 2.6 years ago by
nikos.darzentas
▴ 20
0
votes
0
replies
672
views
Job:
Senior Bioinformatician / Developer (Analysis Pipelines), Earlham Institute, Norwich, UK
bioinformatics
scripting
pipelines
python
Job
updated 2.6 years ago by
GenoMax
99k • written 2.6 years ago by
cschu181
★ 2.6k
0
votes
0
replies
638
views
Job:
Bioinformatician (Analysis Pipelines), Earlham Institute, Norwich, UK
bioinformatics
pipelines
scripting
python
Job
updated 2.6 years ago by
GenoMax
99k • written 2.6 years ago by
cschu181
★ 2.6k
9
votes
6
replies
4.8k
views
Ucsc Genome Browser Automation: Command Line Scripting.
scripting
genome
ucsc
updated 3.1 years ago by
Biostar
20 • written 10.2 years ago by
Devst
▴ 20
0
votes
4
replies
2.6k
views
ImportError: No module named pymol (Windows)
software error
PyMOL
scripting
coding
Python
updated 3.3 years ago by
WouterDeCoster
45k • written 3.3 years ago by
po9.don
• 0
6
votes
2
replies
3.8k
views
Problem Downloading The Nt Database From Ncbi
ncbi
download
scripting
perl
updated 3.5 years ago by
Carlos Borroto
★ 1.9k • written 9.8 years ago by
Anjan
▴ 830
0
votes
0
replies
1.4k
views
Job:
Bioinformatics Scientist in fungal & bacterial genomics at Mascoma/Lallemand (Lebanon, NH)
bioinformatics
scripting
python
R
yeast
Job
4.0 years ago by
rintze.zelle
• 0
1
vote
0
replies
895
views
Job:
Associate Bioinformatician 1 at Partners Personalized Medicine, Cambridge,MA
Python
R
Pipelines
bash
scripting
Job
4.1 years ago by
hns
▴ 150
0
votes
2
replies
1.5k
views
Merlin file format, two markers have the same genetic position
next-gen
software error
scripting
updated 4.1 years ago by
el.zablotskaya
• 0 • written 4.6 years ago by
stu111538
▴ 80
0
votes
0
replies
1.4k
views
PyMol batch computing
protein
pymol
scripting
python
5.2 years ago by
tretyacv
▴ 40
24
votes
20
replies
4.4k
views
9 follow
Perl6 and the Future of Bioinformatics - Compatibility and Integration
programming
scripting
updated 5.6 years ago by
mattoates
▴ 30 • written 5.6 years ago by
Austin
▴ 60
3
votes
6
replies
2.6k
views
Manipulating/Extracting Data and Developing Methods - Language Choice
subjective
programming
scripting
updated 5.6 years ago by
mplace
▴ 40 • written 5.6 years ago by
Austin
▴ 60
11
votes
12
replies
5.4k
views
6 follow
Non-Annotated Long Noncoding Rna Candidates
rna
scripting
updated 6.4 years ago by
angeloulivieri
• 0 • written 9.6 years ago by
Stephanhart
▴ 100
1
vote
2
replies
2.5k
views
From a genome wide predicted CDS annotation file how to remove multiple transcripts and select only one?
bioperl
scripting
sequence edit
updated 6.8 years ago by
Prakki Rama
★ 2.4k • written 6.9 years ago by
cjy8709
• 0
3
votes
2
replies
2.6k
views
Is It Possible To Filter Only Bookend Reads From A Bed File?
bedtools
filtering
scripting
updated 7.2 years ago by
Alex Reynolds
32k • written 7.2 years ago by
Duarte Molha
▴ 230
0
votes
0
replies
1.3k
views
Forum:
Job @ Queen Mary, London, Uk: Genomehacker / Sysadmin As Research Computing Support Officer.
scripting
genomics
Forum
7.4 years ago by
Yannick Wurm
★ 2.3k
0
votes
0
replies
1.5k
views
Job:
Queen Mary, London, Uk: Genomehacker / Sysadmin As Bioinformatics Support Officer
genomics
scripting
Job
7.5 years ago by
Yannick Wurm
★ 2.3k
2
votes
0
replies
2.2k
views
Job:
New Bioinformatician Oppty Supporting A Presitigious Federal Medical Research Center! (Herndon, Va)
bioinformatician
bioinformatics
scripting
linux
sequencing
next-gen
galaxy
Job
7.6 years ago by
Digicon Recruiting
▴ 20
1
vote
2
replies
2.9k
views
How To Get The Plot And Heatmap For The Nucleosome Pattern (Proximity) At +1500 And -1500 From Tss For A List Of Genes?
chipseq
chip-seq
scripting
script
updated 7.8 years ago by
Ming Tang
★ 2.6k • written 7.8 years ago by
sigmagama8
• 0
35
votes
17
replies
18k
views
9 follow
Combining The Paired Reads From Illumina Run
paired
bioperl
scripting
updated 7.9 years ago by
Eric Normandeau
11k • written 10.1 years ago by
Surya Saha
▴ 260
1
vote
0
replies
2.8k
views
Job:
Still Open: Database And Software Developer In Systems Biology/Bioinformatics!
database
bioinformatics
java
scripting
Job
7.9 years ago by
Karin
▴ 50
10
votes
10
replies
5.9k
views
Get Indexes Of Atoms Involved In Dihedral Angles For A Specific Residue In A Pdb File
pdb
protein
structure
scripting
updated 9.2 years ago by
Jonasr
▴ 120 • written 9.2 years ago by
Flow
★ 1.5k
27
votes
16
replies
5.0k
views
Has Anyone Got Plink Working With Gnu Parallel?
plink
parallel
scripting
updated 9.5 years ago by
tange
▴ 190 • written 9.5 years ago by
jvijai
★ 1.2k
18
votes
29
replies
2.4k
views
Script To Print Number Of Occurences Of Genes From Multifasta File
fasta
scripting
updated 9.5 years ago by
Rm
8.0k • written 9.6 years ago by
Syed Imtiyaz
▴ 40
6
votes
7
replies
1.6k
views
How To Check Sequence Type While Downloading
sequence
scripting
biopython
python
updated 9.6 years ago by
Leszek
4.1k • written 9.6 years ago by
Mateusz
▴ 70
12
votes
6
replies
6.8k
views
Multiple Sequence Alignment Score
multiple
bioperl
scoring
scripting
updated 10.1 years ago by
hazratyaaseen
• 0 • written 10.1 years ago by
Lee Katz
★ 3.1k
30
votes
8
replies
5.5k
views
Programming Challange: Pairwise Alignments To Multiple Alignment
alignment
scripting
perl
programming
indel
updated 10.5 years ago by
Haibao Tang
3.0k • written 10.5 years ago by
Rm
8.0k
8
votes
17
replies
5.2k
views
Pymol- Generating Rms Value Of Different Structures
pymol
python
scripting
updated 10.5 years ago by
Michael Schubert
★ 7.0k • written 10.5 years ago by
Thaman
★ 3.3k
39 results • Page
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Recent Votes
Comment: A simple tutorial for a complex ComplexHeatmap
Answer: Hunting invisible characters?
BWA error: no ID within the read group line
Answer: differential expression analysis
Answer: How to verify putative miRNA
Comment: How to make consensus sequence from aligned reads ?
Answer: GSEA for RNA_seq dataset
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Comment: Hunting invisible characters?
by
GenoMax
99k
You could have looked at the file using `cat -vet` which would have shown all characters in the file. Printable and non.
Comment: Can't count features with featurecount
by
avelarbio46
▴ 10
I'm not sure about three things: What does -M and -O do exactly that could benefit in my case? Why should I specify -t if I don't necessa…
Comment: Hunting invisible characters?
by
geneticatt
▴ 120
Thank you, using `dos2unix` worked perfectly!
Answer: Hunting invisible characters?
by
Mensur Dlakic
★ 10k
You may want to read [**this**][1]. I think you may be able to fix your adaper file by typing: dos2unix i5R.txt If an error pops …
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by
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32k
Please do not delete posts that have comments/answers.
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Is there a way to extract ICE bias from balanced .cool file? I know that you can find weight associated with each bin by `cooler dump --bal…
Comment: How to verify putative miRNA
by
boczniak767
▴ 740
Yeah, miRNA could be only verified in wet-lab. Take a look at [stem-loop PCR][1]. I've used it and it works really well. [1]: https://j…
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by
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32k
Because this is a plain copy-paste from the novogene page, it has numbers (pointers to specific references that the source has), but not th…
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by
Mensur Dlakic
★ 10k
This is correct. `X` means any amino acid. Most substitution matrices apply identical penalty (`-1`) when any amino-acid is aligned with X …
Answer: differential expression analysis
by
Mensur Dlakic
★ 10k
I think the numbers you cite are the most extreme values that people will still accept. In most cases I would go for lower p-values (at lea…
Comment: Trimmomatic-0.36 not finding adapter directory
by
willbrown
• 0
The two reads are roughly 23GB each, the only other large output file generated in my last attempt was the trimlog file, which was only 1.5…
Comment: A simple tutorial for a complex ComplexHeatmap
by
ATpoint
48k
You always normalize data before z-scoring it. The Z-score just calculate like the "deviation" of every sample from the mean of all samples…
Answer: GSEA for RNA_seq dataset
by
ATpoint
48k
I tried to explain my understanding of (f)GSEA and why one should use all (expressed) genes here over at this Bioc post: https://support…
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by
willbrown
• 0
I have re-run Trimmomatic for a few hours now, but still no prompt from the terminal. I included '-threads 8' and so expected it to be some…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
Ok thanks a lot. I used the `system(paste0("printf \"\n\" >> Alignment_output/temp.fa"))` after the samtools command and the last command i…
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