Limit : all time
all time today this week this month this year
50 results • Page 1 of 1
Sort: Rank
Rank Views Votes Replies
Showing top results for tag: awk • reset
5
votes
6
replies
2.4k
views
Adding optional tags to a BAM file
RNA-Seq bam sam single-cell awk
updated 15 days ago by 137k • written 2.9 years ago by ▴ 10
20
votes
12
replies
32k
views
7 follow
Forum: When To Use Sed Awk Over Perl Or Python
awk perl python Forum
updated 18 days ago by ▴ 110 • written 7.6 years ago by 8.9k
6
votes
9
replies
986
views
How to generate a combined read count txt file with header as file name
bash linux awk R
updated 19 days ago by • 0 • written 22 months ago by ▴ 340
1
vote
3
replies
221
views
Blast results processing lines bigger than 60
blast unix commands awk result
18 days ago by hdtms ▴ 20
12
votes
5
replies
299
views
how to sort the rows of a file as a matrix?
cut sort awk sed matrix
updated 21 days ago by ★ 3.7k • written 22 days ago by • 0
2
votes
8
replies
263
views
Snakemake. Problem with awk
awk Snakemake
23 days ago by kamanovae ▴ 50
1
vote
4
replies
325
views
bgr files: change chromosome annotation
sed bedgraph expressions awk
updated 5 weeks ago by 52k • written 5 weeks ago by • 0
4
votes
4
replies
287
views
awk, count and print the number of lines following a separator then add value of header to that column
awk
updated 6 weeks ago by 10k • written 6 weeks ago by ▴ 10
1
vote
1
reply
111
views
PDB editing using BASH (Linux)
Renumbering awk BASH PDB
updated 8 weeks ago by ★ 12k • written 8 weeks ago by • 0
5
votes
7
replies
359
views
Creating numbered gene sets from a list of genes
Bash awk geneset
updated 8 weeks ago by 16k • written 8 weeks ago by ▴ 10
6
votes
8
replies
454
views
Extract reads overlapping a specific region in bam file
awk samtools
updated 8 weeks ago by ▴ 660 • written 9 weeks ago by ▴ 460
0
votes
5
replies
208
views
Print rows where the columns have a specific condition
awk linux bash
updated 9 weeks ago by 16k • written 9 weeks ago by ▴ 10
1
vote
2
replies
142
views
How to merge and compare multiple bed files containg some overlaps?
Bedtools awk Bedfile genome
10 weeks ago by JustinZhang ▴ 20
1
vote
4
replies
227
views
vlookup function using awk for two vcf files?
vcf awk vlookup
10 weeks ago by Alexandros.Frydas ▴ 20
0
votes
2
replies
177
views
awk command to print multiple columns
awk
updated 11 weeks ago by 10k • written 11 weeks ago by ▴ 70
2
votes
2
replies
250
views
How to convert (Newick) tree topology without branch length!
sed awk perl
updated 11 weeks ago by 19k • written 11 weeks ago by ▴ 10
0
votes
1
reply
144
views
update fasta header and gff3 file
fasta gff awk header python
updated 11 weeks ago by ▴ 470 • written 11 weeks ago by ▴ 10
0
votes
0
replies
107
views
How to Write same Gene name in column with strain identifier!
awk NJ perl Phylogeny
updated 12 weeks ago by ★ 2.3k • written 12 weeks ago by ▴ 10
6
votes
5
replies
349
views
How to create matrix from row data
sed perl R awk
updated 12 weeks ago by 16k • written 12 weeks ago by ▴ 10
5
votes
5
replies
322
views
How to remove all-N sequence entries from fasta file.
awk perl
updated 3 months ago by 16k • written 3 months ago by ▴ 10
0
votes
2
replies
274
views
Hetero-dimerization analysis with two FASTA files
sequence FASTA python awk bash
updated 3 months ago by 34k • written 3 months ago by ▴ 50
3
votes
3
replies
376
views
how to intersect two files based on three columns
python awk bash
updated 3 months ago by 9.8k • written 3 months ago by ▴ 50
10
votes
18
replies
1.1k
views
How to concatenate FASTA files in a specific order based on sequence ID
sequence fasta awk python pipeline
3 months ago by Apex92 ▴ 50
0
votes
0
replies
174
views
How to perform custom annotation using garfield_annotate_uk10k.sh script in GARFIELD tool?
awk R GWAS bash
4 months ago by bk11 ▴ 40
7
votes
1
reply
280
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk fasta Tutorial
4 months ago by Kevin Blighe 75k
4
votes
5
replies
208
views
Replace fasta Header witha a matching text
awk seqkit grep
updated 4 months ago by 104k • written 4 months ago by ▴ 170
2
votes
3
replies
205
views
want to extract all column which have particular value
extract awk
updated 4 months ago by • 0 • written 4 months ago by ▴ 20
0
votes
0
replies
150
views
How to compare two column from two files with specific condition in awk
awk text-processing
updated 4 months ago by 16k • written 4 months ago by • 0
2
votes
8
replies
181
views
Ignore replacing a comma within quotes
sed awk regex
4 months ago by vinayjrao ▴ 200
4
votes
7
replies
268
views
Fasta and csv file reformatting
sed awk fasta csv
updated 4 months ago by 20 • written 5 months ago by ▴ 390
0
votes
1
reply
223
views
Splitting info field in Annovar's multianno.txt file
Annovar sed awk bcftools
5 months ago by a.j.wilson0000 ▴ 10
3
votes
4
replies
244
views
Remove Extra Info From Fasta Header
fasta RNA-Seq sed awk linux
updated 5 months ago by 104k • written 5 months ago by • 0
2
votes
3
replies
245
views
Find pattern that is present twice and allow <=2 mismatches on each
fastq grep python awk barcode
updated 6 months ago by 16k • written 6 months ago by • 0
5
votes
5
replies
317
views
how to unique a file row-wise?
awk perl sed linux
updated 6 months ago by ★ 1.4k • written 6 months ago by ▴ 70
1
vote
6
replies
242
views
Subseq a FASTA file
awk sed
6 months ago by Explorer ▴ 10
3
votes
3
replies
256
views
Read detection with pattern in paired end FASTQ file
FASTQ paired end Awk
updated 6 months ago by 104k • written 6 months ago by ▴ 20
0
votes
5
replies
260
views
How to filter evidence modeler gene prediction output
gene annotation awk python shell
updated 6 months ago by 19k • written 6 months ago by • 0
2
votes
3
replies
231
views
Compare elements between rows and columns
shell awk RNA-Seq
6 months ago by vinayjrao ▴ 200
19
votes
20
replies
3.3k
views
9 follow
Remove duplicates in an extremely large text file
awk uniq plink SNP
updated 6 months ago by 20 • written 2.5 years ago by ▴ 60
22
votes
17
replies
26k
views
11 follow
Extract fasta sequences from a file using a list in another file.
fasta header extract awk grep
updated 6 months ago by ▴ 420 • written 3.1 years ago by ▴ 20
2
votes
3
replies
332
views
Modify query names longer than 252
samtools fastq awk minimap2
updated 7 months ago by 9.8k • written 7 months ago by • 0
2
votes
2
replies
898
views
Reduce FASTA file name
perl awk fasta genome
updated 24 days ago by 34k • written 5.5 years ago by ▴ 160
28
votes
7
replies
12k
views
Binning Of Chromosome Data
awk
updated 7 months ago by 20 • written 8.2 years ago by ▴ 60
1
vote
3
replies
306
views
Extracting values with certain patterns by searching all columns for each line using "awk"
awk bash unix
updated 7 months ago by 137k • written 7 months ago by ▴ 30
0
votes
3
replies
313
views
How to get transcript ID and tpm from the gtf files of ballgown outputs?
RNA-Seq ballgown hisat2 gtf awk
updated 7 months ago by 34k • written 7 months ago by ▴ 90
3
votes
8
replies
310
views
Split and recombine columns with R
R COG COG annotation annotation awk
updated 7 months ago by ▴ 610 • written 8 months ago by ▴ 50
1
vote
2
replies
339
views
How to make combinations of the values in column 2
combinations random combinations perl awk python
updated 8 months ago by • 0 • written 8 months ago by • 0
1
vote
8
replies
327
views
How to use a bash variable in awk calculation
bash awk
updated 8 months ago by 12k • written 8 months ago by • 0
5
votes
4
replies
308
views
Splitting a semi colon value in new line and copying its neighboring cell values
unix awk python excel
8 months ago by S AR ▴ 70
0
votes
1
reply
250
views
fasta file extraction
fasta sed awk
updated 8 months ago by 16k • written 8 months ago by ▴ 20
50 results • Page 1 of 1
Recent Votes
Comment: opening downloaded files from STRING protein network without R
Comment: What's the biggest thing you dislike about bioinformatics?
Gene Set Enrichment Analysis
Comment: Removing genes of Seurat object during integration pipeline
How to generate a .sam/.bam file of a particular chromosome or even a particular region?
How To Split A Bam File By Chromosome
Comment: I want to make a graph for conserved regions
Recent Locations • All
São Paulo - Brazil - Unifesp, just now
United States, 4 minutes ago
United States, 11 minutes ago
Egypt, 12 minutes ago
United States, 14 minutes ago
Ghana, 16 minutes ago
Villefranche-Sur-Saône, 16 minutes ago
Recent Awards • All
Teacher to WouterDeCoster 45k
Scholar to ATpoint 52k
Teacher to Kevin Blighe 75k
Scholar to Mensur Dlakic ★ 12k
Popular Question to irfanwustl ▴ 20
Teacher to Istvan Albert 88k
Popular Question to finswimmer 14k
Recent Replies
Comment: Displaying points which fall outside of the plot window in EnhancedVolcano by os306 ▴ 10
Hi there, just to follow up on this, I used your package to generate my volcano plots and got exactly what I was looking for. I now wish to…
Comment: inquiry related to snpsift by Kevin Blighe 75k
Hi, please show: 1. the command(s) that you are using 2. a sample of your input data 3. a sample of your output data 4. any status, wa…
Comment: opening downloaded files from STRING protein network without R by fionajcunningham • 0
thanks GenoMax I will try this sorry for delay in reply!! Fiona
Comment: What's the biggest thing you dislike about bioinformatics? by WouterDeCoster 45k
The alternative, constant off-by-one errors, aren't my idea of fun either :-)
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
Yeah, you can filter min_cells in Seurat with SCtransform. That would probably change the gene numbers in the SCT assay of the object. I u…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
Doesn't sctransform has a `min_cells` parameter that you could use here? It will only consider genes detected in at least `min_cells` cells…
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
I was thinking of making it an arbitrary cut off of 10 cells, Seurat's documentation uses 3 for reading in a single sample. I believe that …
Answer: How To Split A Bam File By Chromosome by etiennedanis • 0
With samtools v1.11, ```samtools view -b in.bam chr1 > out.bam``` did not work for me. But ```samtools view -b in.bam 1 > out.bam``` wo…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
What is a "few" cells? So how many? You would need to manually calculate the fraction of cells expressing a certain gene. Not sure in which…
Comment: I want to make a graph for conserved regions by sa.youssef • 0
Thanks so much, it is a great suggestion. may I ask you if you know a way to visualize the results of these data in my report? as we are wo…
Comment: Minfi - estimateCellCounts by Papyrus ★ 1.1k
I understand that you have whole blood samples and that's why you expect them to have more granulocytes? You could also try the [ENmix][1] …
Comment: error related to SnpSift by rheab1230 • 0
I am able to do this. I downloaded the .tar file instead of using conda
Comment: What's the biggest thing you dislike about bioinformatics? by Ram 34k
I'll join you. I am not a fan of python either.
Comment: SNP filtering by Ram 34k
Please pay close attention to [the command I wrote initially][1]. The correct command is `tabix -p vcf GEUVADIS.chr1.genotype.vcf.gz` The `…
Answer: What's the biggest thing you dislike about bioinformatics? by MSRS ▴ 390
The valuable courses which are badly in need but expensive.
Traffic: 1576 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6