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328 results • Page
1 of 7
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Filtering for tag:
awk
•
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
18
replies
543
views
How to concatenate FASTA files in a specific order based on sequence ID
sequence
fasta
awk
python
pipeline
14 days ago by
Apex92
▴ 50
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
7
votes
1
reply
139
views
Tutorial:
Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk
fasta
Tutorial
25 days ago by
Kevin Blighe
72k
4
votes
5
replies
116
views
Replace fasta Header witha a matching text
awk
seqkit
grep
updated 5 weeks ago by
GenoMax
99k • written 5 weeks ago by
Optimist
▴ 160
2
votes
3
replies
133
views
want to extract all column which have particular value
extract
awk
updated 5 weeks ago by
ashishjayamohan
• 0 • written 5 weeks ago by
harry
▴ 20
0
votes
0
replies
107
views
How to compare two column from two files with specific condition in awk
awk
text-processing
updated 5 weeks ago by
cpad0112
15k • written 5 weeks ago by
allods66160
• 0
2
votes
8
replies
111
views
Ignore replacing a comma within quotes
sed
awk
regex
6 weeks ago by
vinayjrao
▴ 200
4
votes
7
replies
182
views
Fasta and csv file reformatting
sed
awk
fasta
csv
updated 6 weeks ago by
Biostar
20 • written 7 weeks ago by
Shaminur
▴ 160
0
votes
1
reply
118
views
Splitting info field in Annovar's multianno.txt file
Annovar
sed
awk
bcftools
8 weeks ago by
a.j.wilson0000
▴ 10
3
votes
4
replies
174
views
Remove Extra Info From Fasta Header
fasta
RNA-Seq
sed
awk
linux
updated 9 weeks ago by
GenoMax
99k • written 9 weeks ago by
kbeavers97
• 0
2
votes
3
replies
158
views
Find pattern that is present twice and allow <=2 mismatches on each
fastq
grep
python
awk
barcode
updated 11 weeks ago by
cpad0112
15k • written 11 weeks ago by
nafizh
• 0
5
votes
5
replies
230
views
how to unique a file row-wise?
awk
perl
sed
linux
updated 12 weeks ago by
dare_devil
★ 1.4k • written 12 weeks ago by
sharmatina189059
▴ 40
1
vote
6
replies
165
views
Subseq a FASTA file
awk
sed
12 weeks ago by
Explorer
▴ 10
3
votes
3
replies
176
views
Read detection with pattern in paired end FASTQ file
FASTQ
paired end
Awk
updated 12 weeks ago by
GenoMax
99k • written 12 weeks ago by
amitpande74
▴ 20
0
votes
5
replies
161
views
How to filter evidence modeler gene prediction output
gene
annotation
awk
python
shell
updated 3 months ago by
Joe
19k • written 3 months ago by
santhoshhegde278
• 0
2
votes
3
replies
165
views
Compare elements between rows and columns
shell
awk
RNA-Seq
3 months ago by
vinayjrao
▴ 200
19
votes
20
replies
2.8k
views
9 follow
Remove duplicates in an extremely large text file
awk
uniq
plink
SNP
updated 3 months ago by
Biostar
20 • written 2.2 years ago by
OAJn8634
▴ 60
20
votes
17
replies
21k
views
11 follow
Extract fasta sequences from a file using a list in another file.
fasta
header
extract
awk
grep
updated 3 months ago by
Rashedul Islam
▴ 390 • written 2.9 years ago by
EBP91
▴ 20
2
votes
3
replies
224
views
Modify query names longer than 252
samtools
fastq
awk
minimap2
updated 3 months ago by
5heikki
9.7k • written 3 months ago by
leonardo.caserta
• 0
2
votes
2
replies
836
views
Reduce FASTA file name
fasta
genome
perl
awk
updated 3 months ago by
Biostar
20 • written 5.2 years ago by
akhilvbioinfo
▴ 160
28
votes
7
replies
12k
views
Binning Of Chromosome Data
awk
updated 3 months ago by
Biostar
20 • written 8.0 years ago by
sheetalshetty13
▴ 60
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
0
votes
3
replies
238
views
How to get transcript ID and tpm from the gtf files of ballgown outputs?
RNA-Seq
ballgown
hisat2
gtf
awk
updated 4 months ago by
Ram
32k • written 4 months ago by
newbie
▴ 90
3
votes
8
replies
219
views
Split and recombine columns with R
R
COG
COG annotation
annotation
awk
updated 4 months ago by
bioinformatics2020
▴ 570 • written 4 months ago by
Sissi
▴ 50
1
vote
2
replies
285
views
How to make combinations of the values in column 2
combinations
random combinations
perl
awk
python
updated 4 months ago by
i-blis
• 0 • written 5 months ago by
debarunacharya
• 0
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
5
votes
4
replies
238
views
Splitting a semi colon value in new line and copying its neighboring cell values
unix
awk
python
excel
5 months ago by
S AR
▴ 60
0
votes
1
reply
193
views
fasta file extraction
fasta
sed
awk
updated 5 months ago by
cpad0112
15k • written 5 months ago by
amitpande74
▴ 20
0
votes
5
replies
219
views
Making disjoint chromosomal sites contiguous with awk
assembly
sequence
awk
bash
bioinformatics
5 months ago by
selplat21
▴ 20
1
vote
6
replies
299
views
Having some regex problems capturing strings with special chars. Could use some help.
sed
awk
regex
updated 5 months ago by
Jorge Amigo
12k • written 5 months ago by
a.j.wilson0000
▴ 10
2
votes
3
replies
193
views
Problems awking columns from map file
awk
unix
map
ped
convertf
updated 6 months ago by
Bastien Hervé
4.9k • written 6 months ago by
Nuthatch
• 0
9
votes
5
replies
225
views
Split delimited text into a new row
sed
awk
grep
updated 6 months ago by
zx8754
10k • written 6 months ago by
Ambika
▴ 40
0
votes
2
replies
249
views
How to remove a break line \n in awk when print the result
awk
bash
linux
download assembly
updated 7 months ago by
Pierre Lindenbaum
135k • written 7 months ago by
xatabadich
• 0
6
votes
10
replies
233
views
Having trouble parsing blast tabular output with awk
awk
blast
tabular
7 months ago by
pawhitesell
▴ 30
3
votes
6
replies
260
views
Extract genes names from GOrilla output file
gO
gene
sed
awk
grep
updated 7 months ago by
rpolicastro
5.1k • written 7 months ago by
rrapopor
▴ 10
2
votes
6
replies
285
views
Running a code in batch mode on a list of files
AWK
GREP
SED
7 months ago by
A
★ 3.9k
2
votes
3
replies
214
views
Replace matching sections of two fastas
fasta
awk
updated 8 months ago by
Pierre Lindenbaum
135k • written 8 months ago by
jamie.pike
▴ 60
2
votes
5
replies
311
views
how to change bam file chromosome names using sed or awk?
bam
awk
updated 8 months ago by
swbarnes2
9.7k • written 8 months ago by
qianxu0517
• 0
6
votes
9
replies
456
views
Split a FastQ file into smaller files
FastQ
bbmap
famas
awk
updated 8 months ago by
GenoMax
99k • written 8 months ago by
Matthias Zepper
▴ 70
6
votes
5
replies
787
views
How to add column to table with awk
awk
bash
shell
unix
bed-files
updated 8 months ago by
Shalu Jhanwar
▴ 490 • written 8 months ago by
linelr
▴ 10
6
votes
7
replies
433
views
awk column number is a variable
RNA-Seq
awk
bash
updated 8 months ago by
user_without_id
▴ 150 • written 8 months ago by
DBScan
▴ 20
0
votes
4
replies
197
views
Extract all seqs bewteen two seqs ID in Fastq
fastq
awk
sed
updated 9 months ago by
Pierre Lindenbaum
135k • written 9 months ago by
erwan.scaon
▴ 820
4
votes
30
replies
455
views
Script makes different file then the manual command, but the command is the same
pipeline
linux
awk
9 months ago by
stan.aanhane
▴ 30
1
vote
3
replies
704
views
MSA ID replacement with a list ID
bash
awk
python
updated 9 months ago by
Biostar
20 • written 3.5 years ago by
lessismore
★ 1.1k
7
votes
8
replies
230
views
Change the field separator
R
awk
field separator
updated 9 months ago by
Jeffin Rockey
★ 1.2k • written 9 months ago by
ATCG
▴ 300
1
vote
3
replies
412
views
renaming fasta file with part of fasta header
awk
sed
updated 9 months ago by
GenoMax
99k • written 9 months ago by
KG
▴ 10
4
votes
4
replies
605
views
How to filter a VCF file with a list of CHR or contig IDs?
vcftools
vcf
chromosome
contigs
awk
updated 10 months ago by
drkennetz
▴ 510 • written 10 months ago by
acoles
▴ 10
4
votes
10
replies
540
views
Comparing multiple columns from 2 files using awk, perl or python
awk
perl
python
10 months ago by
aboozar.soorni
▴ 30
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Comment: Bioinformatics startup market analysis
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I tried to use the SRA toolkit a few months ago, I succesfully installed it and used `prefetch` to get the data, as per their tutorial, but…
Comment: Concatenating fasta files based on prefix ?
by
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15k
If each group has `._1_1.txt.fa` and the pattern is exactly same as in OP, try this: ls *1_1.txt.fa | while read line; do echo ${line%…
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good luck!
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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…
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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…
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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 …
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