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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 9.7k • written 6 days ago by ▴ 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 99k • written 5 weeks ago by ▴ 160
2
votes
3
replies
133
views
want to extract all column which have particular value
extract awk
updated 5 weeks ago by • 0 • written 5 weeks ago by ▴ 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 15k • written 5 weeks ago by • 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 20 • written 7 weeks ago by ▴ 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 99k • written 9 weeks ago by • 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 15k • written 11 weeks ago by • 0
5
votes
5
replies
230
views
how to unique a file row-wise?
awk perl sed linux
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by ▴ 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 99k • written 12 weeks ago by ▴ 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 19k • written 3 months ago by • 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 20 • written 2.2 years ago by ▴ 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 ▴ 390 • written 2.9 years ago by ▴ 20
2
votes
3
replies
224
views
Modify query names longer than 252
samtools fastq awk minimap2
updated 3 months ago by 9.7k • written 3 months ago by • 0
2
votes
2
replies
836
views
Reduce FASTA file name
fasta genome perl awk
updated 3 months ago by 20 • written 5.2 years ago by ▴ 160
28
votes
7
replies
12k
views
Binning Of Chromosome Data
awk
updated 3 months ago by 20 • written 8.0 years ago by ▴ 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 135k • written 4 months ago by ▴ 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 32k • written 4 months ago by ▴ 90
3
votes
8
replies
219
views
Split and recombine columns with R
R COG COG annotation annotation awk
updated 4 months ago by ▴ 570 • written 4 months ago by ▴ 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 • 0 • written 5 months ago by • 0
1
vote
8
replies
255
views
How to use a bash variable in awk calculation
bash awk
updated 5 months ago by 10k • written 5 months ago by • 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 15k • written 5 months ago by ▴ 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 12k • written 5 months ago by ▴ 10
2
votes
3
replies
193
views
Problems awking columns from map file
awk unix map ped convertf
updated 6 months ago by 4.9k • written 6 months ago by • 0
9
votes
5
replies
225
views
Split delimited text into a new row
sed awk grep
updated 6 months ago by 10k • written 6 months ago by ▴ 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 135k • written 7 months ago by • 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 5.1k • written 7 months ago by ▴ 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 135k • written 8 months ago by ▴ 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 9.7k • written 8 months ago by • 0
6
votes
9
replies
456
views
Split a FastQ file into smaller files
FastQ bbmap famas awk
updated 8 months ago by 99k • written 8 months ago by ▴ 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 ▴ 490 • written 8 months ago by ▴ 10
6
votes
7
replies
433
views
awk column number is a variable
RNA-Seq awk bash
updated 8 months ago by ▴ 150 • written 8 months ago by ▴ 20
0
votes
4
replies
197
views
Extract all seqs bewteen two seqs ID in Fastq
fastq awk sed
updated 9 months ago by 135k • written 9 months ago by ▴ 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 20 • written 3.5 years ago by ★ 1.1k
7
votes
8
replies
230
views
Change the field separator
R awk field separator
updated 9 months ago by ★ 1.2k • written 9 months ago by ▴ 300
1
vote
3
replies
412
views
renaming fasta file with part of fasta header
awk sed
updated 9 months ago by 99k • written 9 months ago by ▴ 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 ▴ 510 • written 10 months ago by ▴ 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
328 results • Page 1 of 7
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Comment: Bioinformatics startup market analysis
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Recent Replies
Comment: How to download raw sequence data from GEO/SRA by cicindel ▴ 60
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 cpad0112 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%…
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.
Comment: question when using topgo 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? by cpad0112 15k
is it `log10p` or `-log10p` on y-axis?
Answer: How to get GO terms to specific to perticular biological process 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 …
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