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407 results • Page
1 of 9
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Filtering for tag:
bash
•
reset
0
votes
0
replies
48
views
Hetero-dimerization analysis with two FASTA files
sequence
bash
awk
python
FASTA
4 days ago by
Apex92
▴ 50
3
votes
3
replies
186
views
how to intersect two files based on three columns
python
awk
bash
updated 6 days ago by
5heikki
9.7k • written 6 days ago by
Apex92
▴ 50
10
votes
15
replies
642
views
conda install -c bioconda simlord | SimLoRD
ubuntu
bash
SimLoRD
reads
fastq
8 days ago by
Daniel Bell
▴ 10
0
votes
4
replies
271
views
Replace headers of fasta while with simplified headers from another file
python
fasta
bash
updated 10 days ago by
cpad0112
15k • written 10 days ago by
Ava
• 0
9
votes
11
replies
503
views
Bash loop for bbduk
bash
bbduk
updated 10 days ago by
cpad0112
15k • written 10 days ago by
avelarbio46
▴ 10
3
votes
7
replies
173
views
bash: sudo: command not found | ea-utils installation [CLOSED]
fastq
ea-utils
reads
bash
linux
10 days ago by
Daniel Bell
▴ 10
3
votes
4
replies
140
views
bash: conda: command not found | for SimLord [CLOSED]
windows
bash
simlord
miniconda
updated 10 days ago by
GenoMax
99k • written 11 days ago by
Daniel Bell
▴ 10
0
votes
4
replies
291
views
Puzzling Bowtie2 Input Error -S flag
bash
bowtie2
alignment
shell
16 days ago by
geneticatt
▴ 110
0
votes
0
replies
85
views
How to perform custom annotation using garfield_annotate_uk10k.sh script in GARFIELD tool?
awk
R
GWAS
bash
20 days ago by
bk11
▴ 40
12
votes
10
replies
540
views
9 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 21 days ago by
Juke34
★ 5.3k • written 21 days ago by
Kumar
▴ 50
11
votes
13
replies
5.3k
views
Bash scripting FastQC for multiple fastq files in multiple directories
RNA-Seq
bash
fastQC
updated 25 days ago by
dare_devil
★ 1.4k • written 2.5 years ago by
rc1253
▴ 20
0
votes
3
replies
142
views
Read VEP output from command line in R
vep
ensembl
R
Bash
updated 27 days ago by
prasundutta87
▴ 470 • written 27 days ago by
yussab
▴ 30
1
vote
16
replies
716
views
FeatureCounts output does not contain all the genes in the annotation file
FeatureCounts
RNASeq
Rice
Bash
updated 5 weeks ago by
el.dansch
• 0 • written 10 months ago by
devbt15
▴ 10
2
votes
6
replies
178
views
Split multiallelic SNPs to biallelic from vcf
python
R
bash
vcf
6 weeks ago by
User000
▴ 440
0
votes
6
replies
184
views
Phasing vcf file with Beagle
vcf
phasing
beagle
haplotype
bash
7 weeks ago by
sixthirty
• 0
7
votes
6
replies
210
views
nohup with while loop
bash
loop
SRAtoolkit
7 weeks ago by
pt.taklifi
▴ 60
3
votes
5
replies
199
views
How to parse protein and dna sequences from prokka generated gbk or gff file based on locus_tag?
genome
perl
python
bash
R
updated 7 weeks ago by
Mensur Dlakic
★ 10k • written 7 weeks ago by
Kumar
▴ 50
1
vote
5
replies
175
views
mummerplot results interpretation
mummer
mummerplot
alignment
bash
7 weeks ago by
langziv
• 0
3
votes
8
replies
132
views
Merging .fq files per sample using a big loop - BASH?
bash
merging samples
fastq files
genomics
loop
updated 8 weeks ago by
lieven.sterck
10k • written 8 weeks ago by
giulia.trauzzi
• 0
1
vote
6
replies
228
views
Using GNU parallel to speed up merging VCFs with bcftools
vcf
parallel
gwas
bcftools
bash
8 weeks ago by
mfshiller
▴ 10
4
votes
8
replies
547
views
No space left on device error with deeptools bamCompare
software error
deeptools
picard
bash
terminal
updated 8 weeks ago by
Kevin Blighe
72k • written 8 months ago by
jennxyzhang
• 0
0
votes
2
replies
138
views
system commands from R containing single and double quotes
R
bash
9 weeks ago by
joe
▴ 180
1
vote
7
replies
181
views
Extract longest transcript from Ensembl gene table
bash
gene
ensembl
R
9 weeks ago by
Midge
• 0
0
votes
2
replies
235
views
How to run different fasta files in a same process with its output respective
bash
sequence
linux
9 weeks ago by
diego1530
▴ 40
0
votes
0
replies
240
views
Mutual Information for a collection of FASTA files
python
fasta
bash
mutualinformation
sequence
11 weeks ago by
nameuser
▴ 30
2
votes
4
replies
143
views
bash find consecutive acc. no. & insert text
bash
acc.no.
efetch
NCBI
12 weeks ago by
6schulte
▴ 30
1
vote
2
replies
186
views
Pipelines in bash vs other languages
pipeline
bash
python
3 months ago by
jaynishshah
• 0
15
votes
13
replies
382
views
How to extract a sequence below a fasta header (">") from a fasta file ?
fasta
bash
updated 3 months ago by
ATpoint
47k • written 3 months ago by
v.berriosfarias
▴ 10
1
vote
3
replies
198
views
how to filter sequence database with bash?
sequencing
database
bash
FASTA
grep
updated 3 months ago by
Jorge Amigo
12k • written 3 months ago by
Lisa Prudnikow
• 0
5
votes
4
replies
243
views
Get the top X number of lines per unique value in one column, once you've sorted a text file using 'sort'
bash
shell
sort
updated 3 months ago by
GenoMax
99k • written 3 months ago by
niccolo.alfano
• 0
3
votes
3
replies
231
views
Help with parallelization and loop cutadapt
bash
cutadapt
loop
updated 3 months ago by
Dave Carlson
▴ 610 • written 3 months ago by
russell.stewart.j
▴ 20
5
votes
7
replies
194
views
Merging same one column different files
merge
bash
updated 3 months ago by
Pierre Lindenbaum
135k • written 3 months ago by
melania 2282
▴ 100
6
votes
8
replies
212
views
How to extract header from within the data (line of a file)
data extraction
bash
data processing
4 months ago by
6schulte
▴ 30
1
vote
3
replies
226
views
Extracting values with certain patterns by searching all columns for each line using "awk"
awk
bash
unix
updated 4 months ago by
Pierre Lindenbaum
135k • written 4 months ago by
ClkElf
▴ 30
2
votes
7
replies
238
views
Merging lots of csv files in on master one
bash
csv
updated 4 months ago by
steve
★ 2.9k • written 4 months ago by
psschlogl
▴ 30
8
votes
11
replies
7.2k
views
8 follow
Faster way to get GC content and Coverage from .fasta
sequencing
next-gen
genome
bash
fasta
updated 4 months ago by
mendozamejian
▴ 10 • written 3.1 years ago by
Shred
▴ 300
4
votes
4
replies
238
views
Blast run fails: memory exceeds the limit
bash
blast
blastx
updated 4 months ago by
Mensur Dlakic
★ 10k • written 4 months ago by
langziv
• 0
0
votes
1
reply
138
views
Tools to find similarity and identity via terminal or ubuntu
sequencing
genome
alignment
bash
linux
4 months ago by
USER
• 0
0
votes
0
replies
185
views
locuszoom on a HPC - LD could not be computed for SNP
locuszoom
HPC
bash
GWAS
4 months ago by
tacrolimus
▴ 80
1
vote
4
replies
171
views
how can I write a script for calculate snp variants coverage
script
bash
genomecoverage
variantcoverage
4 months ago by
tacidilceren
• 0
3
votes
1
reply
273
views
Masking Y chromosomes
genome
whole generation sequencing
wgs
bash
updated 5 months ago by
Jorge Amigo
12k • written 5 months ago by
lamia_203
▴ 90
1
vote
8
replies
255
views
How to use a bash variable in awk calculation
bash
awk
updated 5 months ago by
lieven.sterck
10k • written 5 months ago by
nadarajan_v
• 0
2
votes
6
replies
549
views
How to execute curl with dynamically created URL using Bash
bash
updated 5 months ago by
zorbax
▴ 250 • written 5 months ago by
nadarajan_v
• 0
0
votes
3
replies
221
views
How to remove low abundance and less prevalent data from my dataset?
metagenome
bash
5 months ago by
deep771992chanda
▴ 30
4
votes
6
replies
212
views
where to practise bash
bash
programming
learning
updated 5 months ago by
JC
12k • written 5 months ago by
gubrins
▴ 70
3
votes
6
replies
271
views
filtering column based on column header from a file
bash
linux
R
updated 5 months ago by
Sam
★ 3.4k • written 5 months ago by
Bioinfonext
▴ 320
2
votes
2
replies
154
views
Filter files based on number in the filenames
regex
bash
updated 5 months ago by
zx8754
10k • written 5 months ago by
vanessagpds
▴ 10
1
vote
1
reply
172
views
Bulk extraction of cis-elements (TFBS) from Softberry output
python
bash
5 months ago by
venura
▴ 70
4
votes
7
replies
252
views
Merge coordinates by gene ID
BEDOPS
BASH
BEDTOOLS
BED
5 months ago by
r.tor
▴ 50
0
votes
0
replies
203
views
DeepMAsED installation and dependencies
DeepMAsED
bash
tensorflow
scipy
5 months ago by
v.berriosfarias
▴ 10
407 results • Page
1 of 9
Recent Votes
Comment: Bioinformatics startup market analysis
Concatenating fasta files based on prefix ?
Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
Comment: Concatenating fasta files based on prefix ?
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Recent Replies
Comment: Bioinformatics startup market analysis
by
grant.hovhannisyan
★ 2.1k
good luck!
Comment: Bioinformatics startup market analysis
by
gtechbio
▴ 30
Dear @juanjo75es, thank you for your input. We do agree that NGS data/metadata should be more accessible to public, in part also due to ini…
Comment: Bioinformatics startup market analysis
by
gtechbio
▴ 30
Dear @grant.hovhannisyan, thank you for the advice. In fact we are already in touch with two local genomics facilities, though as you have …
Answer: No annotation peaks when running homer
by
geneticatt
▴ 110
Try raising your p-value to make sure that they aren't all just being filtered out by that threshold (which seems pretty low). Edit: I may…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
It looks like the following: system(paste0("mafft --anysymbol --maxiterate 1000 Alignment_output/",GENE,".fa > ",GENE,".mafft.fa")) GE…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
Yes, I am using the following loop first in R to process all the files. This is the code that I am running first: blastn.filelist <- s…
Comment: Bioinformatics startup market analysis
by
grant.hovhannisyan
★ 2.1k
agreed, especially if no private information (names, clinical status, etc) is needed, this information should be freely accessible.
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by
Kevin Blighe
72k
^^ this
Answer: question when using topgo
by
seidel
7.6k
The GenTable() function has a parameter called *numChar* that controls this: "the GO term definition will be truncated such that only the f…
Comment: why my volcano plot looks strange?
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cpad0112
15k
is it `log10p` or `-log10p` on y-axis?
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by
geneticatt
▴ 110
See the 'is_a' field in the go.obo file. If you're looking for all subcategories of GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl…
Comment: How to perform multiple alignment using MAFFT?
by
Dunois
▴ 620
What does your `system()` command look like now, after having added `--anysymbol`? I am guessing you added `--anysymbol` right before that …
Comment: How to perform multiple alignment using MAFFT?
by
Ram
32k
Are you using this statement in a loop? If so, please refine your command to error out with the file that produces the error - maybe print …
Answer: How to obtain FDR across all regions investigated in DiffBind
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The "correct" way to retrieve results in `DiffBind` is via the `dba.report()` function. Setting `th=1` returns all results with FDR <= 1.0,…
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If you run `RUVseq` on the data from study B only, you'd get predicted values for age and sex but these will be numerical. I suppose you co…
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