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Showing top results for tag:
script
•
reset
2
votes
21
replies
556
views
How to loop on two fasta files for hetero-dimerization analysis
fasta
script
python
sequence
updated 7 days ago by
cpad0112
15k • written 7 days ago by
Apex92
▴ 50
0
votes
2
replies
145
views
IF statement (in linux script) to merge Fastq files with similar (but not the same) names
unix
script
ifstatement
linux
fastq
updated 16 days ago by
cpad0112
15k • written 16 days ago by
endretoth
▴ 20
0
votes
0
replies
108
views
How can I extract information from tRNA encoding genes only (Python)?
Python
gc3
script
6 weeks ago by
amirah.rafique
• 0
0
votes
5
replies
153
views
About shell script
script
alignment
updated 9 weeks ago by
zx8754
10k • written 9 weeks ago by
r00628112
▴ 10
2
votes
6
replies
199
views
Blast + Alignement Shell Script
alignment
script
blast
shell
Tutorial
updated 12 weeks ago by
brian.fristensky
▴ 160 • written 12 weeks ago by
florian.grosmaire
• 0
2
votes
6
replies
276
views
problem use htseq-count in bash script
htseq-count
script
4 months ago by
o.omidan
▴ 10
1
vote
4
replies
175
views
how can I write a script for calculate snp variants coverage
script
bash
genomecoverage
variantcoverage
5 months ago by
tacidilceren
• 0
0
votes
5
replies
1.2k
views
Calculate numbers of indels <=2 nt within sam
script
updated 5 months ago by
Biostar
20 • written 3.8 years ago by
Rox
★ 1.3k
0
votes
6
replies
1.5k
views
Split one embl file into several
script
python
perl
updated 7 months ago by
Biostar
20 • written 5.8 years ago by
thom_otis
• 0
6
votes
4
replies
448
views
Script to obtain human protein sequences by the gene symbols
script
gene
protein
updated 8 months ago by
user_without_id
▴ 150 • written 10 months ago by
Shicheng Guo
★ 8.6k
11
votes
10
replies
4.4k
views
Errors In A Bioperl Script, Please Help Me To Have A Check, Thanks In Advance!
bioperl
script
blast
updated 9 months ago by
Biostar
20 • written 7.9 years ago by
xiongtl2013
▴ 40
3
votes
3
replies
239
views
Error python script overlapping_reads.py
python
script
github
11 months ago by
Amaranta Remedios
▴ 10
0
votes
2
replies
229
views
BLAST and GFF script to find locations of SNPs
BLAST
gff
script
SNP
11 months ago by
Kiki_01
• 0
4
votes
7
replies
343
views
bash bowtie script output with prefix
bash
script
unix
updated 11 months ago by
Joe
19k • written 11 months ago by
Amaranta Remedios
▴ 10
2
votes
4
replies
685
views
Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
hmm
hmmer
protein domain
bash
script
updated 12 months ago by
Mensur Dlakic
★ 10k • written 12 months ago by
O.rka
▴ 290
0
votes
0
replies
281
views
HMMSCAN error in batch submission
bash
HMM
script
13 months ago by
geizetomazetto
• 0
1
vote
2
replies
597
views
Prokka Python Script for Gene Annotation
Python
Prokka
Script
Annotation
Linux
updated 16 months ago by
Mensur Dlakic
★ 10k • written 16 months ago by
Fid_o
▴ 20
3
votes
3
replies
347
views
Python to R
python
R
CODE
Script
Convert
written 16 months ago by
vschultz
• 0
2
votes
4
replies
415
views
Results of two sequential bash pipes into a variable instead of a file?
bash
pipe
variable
shell
script
updated 16 months ago by
Biostar
20 • written 18 months ago by
normanreppingen
• 0
3
votes
8
replies
384
views
Converting amino acid sequences to numerical values
R
perl
python
sequence
script
updated 17 months ago by
JC
12k • written 17 months ago by
karish03
▴ 10
1
vote
5
replies
375
views
Merge overlapping intervals in a bed file containing different chromosomes
merge
bed
script
updated 18 months ago by
Pierre Lindenbaum
135k • written 18 months ago by
dzisis1986
▴ 20
1
vote
2
replies
348
views
Help with Python script
python
script
updated 19 months ago by
GenoMax
99k • written 19 months ago by
imda
▴ 10
0
votes
3
replies
299
views
Inserting bash and bioinformatic's scripts into browser database
browser
script
bash
java
python
19 months ago by
flogin
▴ 250
9
votes
9
replies
2.2k
views
Perl loop woes
script
perl
for loop
ortho groups
phylogentics
updated 21 months ago by
Biostar
20 • written 2.8 years ago by
jt500
• 0
1
vote
7
replies
521
views
intersection for several file
RNA-Seq
sequencing
script
updated 23 months ago by
manuel.belmadani
★ 1.3k • written 23 months ago by
mxlsherry1992
▴ 40
9
votes
13
replies
1.2k
views
Python Script to map reads to reference sequence
sequence
python
mapping
script
reference sequence
24 months ago by
Fid_o
▴ 20
4
votes
6
replies
2.2k
views
Create a plot based on binary input of 1s and 0s.
R
script
plot
updated 2.0 years ago by
zx8754
10k • written 2.0 years ago by
Inquisitive8995
▴ 210
2
votes
4
replies
506
views
Is it possible to print DNA sequences of subject organism in tblastn?
BLAST
alignment
tblastn
sequence analysis
script
2.0 years ago by
Kumar
▴ 50
4
votes
2
replies
562
views
Help with iTol annotation python script
python
itol
script
updated 2.0 years ago by
cschu181
★ 2.6k • written 2.0 years ago by
heuristic
• 0
4
votes
5
replies
739
views
Blast script over multiple databases
blastn
script
multipledatabases
2.1 years ago by
dllopezr
▴ 60
5
votes
4
replies
513
views
Writing scripts for a single vs all chromosomes
RNA-Seq
script
shell
2.1 years ago by
Antonio.Aubry
▴ 10
0
votes
2
replies
652
views
Read In Function for BAM file processing
Script
BAM
2.1 years ago by
Jonas.Koch
• 0
11
votes
18
replies
1.2k
views
6 follow
How to extract filename and change text in the same file
sequence
VCF
Script
updated 2.1 years ago by
Malcolm.Cook
★ 1.2k • written 2.1 years ago by
Inquisitive8995
▴ 210
1
vote
2
replies
1.8k
views
Bash script iterating over 2 arrays
bash
script
loops
multiple arrays
2.1 years ago by
mdriskil
▴ 10
2
votes
3
replies
608
views
Bash and seqret problem
bash
seqret
script
2.2 years ago by
MichaelTrev
▴ 10
0
votes
1
reply
1.2k
views
Problem installing GATK
GATK
script
software error
Ubuntu
updated 2.2 years ago by
finswimmer
14k • written 2.2 years ago by
j.e.kelly
• 0
8
votes
7
replies
8.5k
views
TrimGalore! on multiple paired fastq files
rna-seq
trimgalore!
paired-end
script
updated 2.2 years ago by
rogangrant2022
▴ 10 • written 4.5 years ago by
emblake
▴ 60
0
votes
8
replies
808
views
how to change the sequence ID and order of sequences in a file to match an alignment output file
python
script
updated 2.2 years ago by
shenwei356
5.8k • written 2.2 years ago by
Kay
▴ 10
0
votes
10
replies
807
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 2.3 years ago by
Biostar
20 • written 2.4 years ago by
BetterOrWorse
• 0
2
votes
4
replies
670
views
How to change the path so that screen can take the default python path?
python
script
issue
updated 2.4 years ago by
Jeffin Rockey
★ 1.2k • written 2.4 years ago by
saadleeshehreen
▴ 70
3
votes
2
replies
575
views
Python script strange behavior
python
script
2.5 years ago by
dllopezr
▴ 60
8
votes
13
replies
1.1k
views
Editing fasta headers with bash
fasta headers
fasta
bash
script
updated 2.6 years ago by
Joe
19k • written 2.6 years ago by
James
▴ 20
17
votes
10
replies
2.7k
views
6 follow
Extract only rows with main chromosomes (1-22, X, Y) on first column?
linux
grep
R
script
updated 2.6 years ago by
benformatics
★ 2.1k • written 2.7 years ago by
star
▴ 270
1
vote
4
replies
587
views
merge multiple data with multiple columns?
linux
script
2.7 years ago by
star
▴ 270
2
votes
2
replies
514
views
collapsing GFF coordinates with common start OR stop
GFF
parse
script
bedtools
Perl
updated 2.7 years ago by
h.mon
32k • written 2.7 years ago by
Anand Rao
▴ 350
1
vote
3
replies
568
views
Reconstruct bed file from tab
R
chr
script
python
updated 2.7 years ago by
ATpoint
48k • written 2.7 years ago by
dzisis1986
▴ 20
6
votes
7
replies
1.4k
views
How can I parse arguments from a config file to create a command line menu in R ?
R
arguments
script
updated 2.7 years ago by
Joe
19k • written 2.7 years ago by
dzisis1986
▴ 20
6
votes
8
replies
911
views
Remove hypothetical proteins
FASTA
script
grep
updated 2.8 years ago by
Ram
32k • written 2.8 years ago by
biodano.geo
▴ 20
12
votes
11
replies
682
views
script for task or AWK
script
awk
updated 2.8 years ago by
dariober
12k • written 2.8 years ago by
rob234king
▴ 600
0
votes
4
replies
621
views
How to download FASTA file from psRNAtarget
sequence
FASTA
download
batch
script
2.9 years ago by
ebrahimi.re67
• 0
50 results • Page
1 of 1
Recent Votes
Answer: R command worked yesterday, but stalls today?
Comment: How to combine 2 incomplete GTF
Answer: comprehensive bacterial phylogenetic tree with edge lengths for all of RefSeq or
Comment: How can I Extract Transposable element from a new genome assembly?
Answer: How to combine 2 incomplete GTF
Answer: How to combine 2 incomplete GTF
A: Correct Way To Parse A Fasta File In Python
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Recent Awards •
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Teacher
to
JC
12k
Commentator
to
Nicolas Rosewick
9.3k
Voter
to
cmo
▴ 70
Scholar
to
Juke34
★ 5.3k
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to
rafaelsolersanblas
▴ 70
Teacher
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Michael Dondrup
48k
Commentator
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Joe
19k
Recent Replies
Comment: how to select peaks at not transcribed genes
by
Lila M
▴ 910
indeed, my IP was for Pol2
Comment: R command worked yesterday, but stalls today?
by
dariober
12k
...besides, [wget](https://www.gnu.org/software/wget/manual/wget.html) has a `-c/--continue` option to resume the download of a partial fil…
Comment: how to select peaks at not transcribed genes
by
jared.andrews07
9.3k
What makes you think genes with a peak are transcribed while those without are not? Unless your IP was for Pol2, this is an overly simplist…
Comment: How to combine 2 incomplete GTF
by
rafaelsolersanblas
▴ 70
Thank you! I am going to try it :)
Comment: How to combine 2 incomplete GTF
by
GenoMax
99k
Please create a new environment when installing packages. That avoids conflicts. conda create -c bioconda -n agat agat conda acti…
Comment: How to combine 2 incomplete GTF
by
rafaelsolersanblas
▴ 70
Hi Juke, I am trying to install it and I can't. ![enter image description here][1] [1]: /media/images/bc08978b-10f7-4666-b385-57807b…
Comment: comprehensive bacterial phylogenetic tree with edge lengths for all of RefSeq or
by
cmo
▴ 70
I agree with you, Mensur, that the GTDB is arguably more reliable and comprehensive than NCBI. However, due to the relative greater longevi…
Comment: how to select peaks at not transcribed genes
by
Lila M
▴ 910
rigth, it is a ChIP seq analysis
Comment: how to select peaks at not transcribed genes
by
ATpoint
48k
Which type data are we talking about? What was the experiment? There are literally no details in this question right now. It the assay meas…
Comment: How to combine 2 incomplete GTF
by
rafaelsolersanblas
▴ 70
Thank yo so much Juke!
Comment: MASURCA output
by
kilcdincer
▴ 10
Thank you. I understood ploidy part. My genome is supposed to belong to diploid Candida albicans. And genome size of diploid Candida alb…
Answer: How to combine 2 incomplete GTF
by
Juke34
★ 5.3k
To give more precision to the @genomax comment: `agat_sp_compare_annotations.pl` will tell you the differences. Then you can choose to …
Comment: GSEA for RNA_seq dataset
by
ATpoint
48k
No problem. I am not really familiar with what the GSEA implementation from the Broad institute does. I personally use fgsea from Bioconduc…
Comment: How to combine 2 incomplete GTF
by
rafaelsolersanblas
▴ 70
Thank you!! I will try it :)
Comment: how to select peaks at not transcribed genes
by
Lila M
▴ 910
you mean in the call peaks? And what are those 232 not annotated peaks?aren't they tss associated to not transcribed genes?
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