Questions tagged [awk]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
2
votes
2answers
47 views

Extracting specific sections from FASTQ determined by positions

Given a FASTQ file, I'd like to generate a new FASTQ file including only certain subsections of the original sequences specified by their positions. For example, say I want to extract the ...
1
vote
1answer
79 views

awk shell script

I have a folder named quant. Inside this folder I have 27 folders named SRR8068516_quant to SRR8068543_quant. I want to edit a file inside these folders titled quant.sf and produce an output. I ...
1
vote
1answer
51 views

remove sequences from fasta file matching a string in the header

I have a file with 16S sequences. some headers contain species information. For my purposes I would like to exclude a number of species from the file, therefore I would like to do a pattern matching ...
-5
votes
1answer
96 views

How I reformat this data [closed]

I have this data all is one line even gene from first sample joined the second one while I want this data column wise each field separated like I have provided ...
-4
votes
1answer
46 views

Joinning columns from different files

I have 48 files in which I have r1 ...
1
vote
2answers
41 views

Trying to divide number in fourth TSV column by a certain number according to its corresponding identifier in the first column

I was wondering if anyone could help with my little issue in manipulating tsv files in order to calculate estimated coverage across many tsv files. I have tsv files that look something like this: <...
1
vote
3answers
101 views

Edit all the fasta headers using awk

kindly your comment highly appreciated have more than 4k header sequences look like: ...
1
vote
1answer
33 views

how to calculate coverage of each base of mapped reads?

I have a RNA aligned file without any header info. I need to calculate the coverage of each mapped base for per chromosome. Is it possible to do it with perl ? ...
1
vote
4answers
135 views

How I can change the name of multiple files at once in R or terminal?

I have 200 .vcf files in a folder with long names like LP6005409-DNA_E03_vs_LP6005408-DNA_E03.snp.pass.vcf How can I change the name of each file to, for ...
1
vote
2answers
52 views

How to merge two files on the first 3 columns?

I have two files that look like this: ...
0
votes
1answer
53 views

awk find pattern

I am trying to find this pattern on a large file but the output doesn't look good. The output doesn't seem to reflect the pattern. ...
0
votes
3answers
65 views

match two files and check if position of chrom is within exon region

I have two files, file1 and file2. I want to match file1 chrom with ...
0
votes
4answers
71 views

Merging two files together

Is it possible to merge two files together using awk? I have two files with matched Chrom and pos column file1 has the columns ...
0
votes
1answer
45 views

Filter out other character after the genotype

Is it possible to filter out all the characters that come after the genotype, for example, I have a data ...
1
vote
1answer
44 views

awk find Sickle cell anemia from father, mother, son, daughter

I have a file where i what to check for a pattern below and print out all the lines that matches the pattern but the output is empty. here is the pattern that i am looking for. Father = 1/0 or 0/1 ...
4
votes
3answers
112 views

awk working with large files

I have two very large vcf files 2GB and 6GB I want to look for unique combinations of CHROM and POS and output the row that matches. However, because the files a so large my machine always hang and ...
1
vote
4answers
134 views

split 1 column input into 5 column bed file

In f1 below I am trying to split $1 based on each line and create a bed file. If the line is a snp then the ...
2
votes
2answers
207 views

Filter reads belonging to unique sequences with threshold

I have CLL samples as fastq files and I want to remove those reads which have a unique sequence with less than 10 read counts each. I tried this by following way using awk to make it faster: ...
0
votes
1answer
260 views

How to extract all pair end fastq.gz files from multiple subdirectory to a single folder

I have all file names for each paired-end fastq pair as shown below. Could you please suggest how I can extract all fastq.gz files in a single folder? sample name: ...
1
vote
2answers
76 views

How to extract values from second file on the basis common first column?

File1: ENST00000000233 ARF5 ENST00000000412 M6PR ENST00000001008 FKBP4 ENST00000001146 CYP26B1 ENST00000002501 DBNDD1 ENST00000002596 HS3ST1 File 2: ...
1
vote
2answers
48 views

awk for motif splicing from an amino acid alignment

I'm looking to splice out specific amino acid alignment positions as a continuous motif from an alignment (~15 000 sequences). The code is written in Perl (I agree not many developers now) but ...