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Questions tagged [awk]

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1answer
44 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
60 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
62 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
41 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
38 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
98 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
115 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
81 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
87 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
69 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
39 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 ...