Use this tag for questions relating to common bioinformatics tasks performed on a *nix system. Things like manipulating/converting between standard biological text formats, extracting data of interest from such formats etc.

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38 views

Drawing a histogram from a bash command output

I have the following output from a miRNA Predictor: Read Sequence:hsa-miR-576-3p MIMAT0004796 (22 nt) Read Sequence:gi|182396|gb|M74088.1|HUMFAPAPC Human APC gene mRNA, complete cds (8972 nt) ...
2
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2answers
87 views

filter blast output for e value

I ran a BlastX against the SwissProt database in with an -evalue threshold of 1e-3. The output looks like: >TCONS_00006082 sp|P43298|TMK1_ARATH 57.89 57 23 2 459 292 751 ...
4
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2answers
596 views

Nested 'awk' in a 'while' loop, parse two files line by line and compare column values

I need some help with a combination of awk & while loop. I have two simple files with columns (normal ones are very large), one representing simple intervals for an ID=10(of coding ...
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2answers
125 views

for loop when matching both front and back of file name

I'm trying to set up a for loop to run a process on pairs of files. The names of the files look like this 36_002_CGATGT_L001_R1_005.fastq.gz 36_002_CGATGT_L001_R2_005.fastq.gz ...
0
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1answer
103 views

Creating a list containing filenames with paths

I have a directory(INPUTDIR) with sample names as subdirectories(508_C,540_C,570_D etc).Within those each subdirectories there is another directory called FASTQ which contains two kinds of files. ...
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3answers
128 views

match just one row in two files and return the whole column from file 2

If I have two files file1: Reference Position 905894 1197693 3703749 92108275 114940633 114940633 file2: Mapping Reference Position Type Length Reference Allele Linkage Zygosity Count ...
1
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1answer
99 views

Retrieving fasta sequences using bed file information from locally installed file

I have a .bed file containing around 30000 rows for which I have the sequences retrieved using fetch-sequences module of the rsat tool (http://rsat.ulb.ac.be/rsat/help.fetch-sequences.html#usage). ...
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2answers
374 views

Merge fields in a file

I have a file with 7 columns, a GFF file having chromosomal regions.I want to collapse the rows where REGION ="exon" to only one row in the file.The row has to be collapsed on the basis of regions ...
5
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1answer
584 views

counting multiple patterns in a single pass with grep?

I've written a grep loop to iteratively count DNA trinucleotides within a gzipped DNA fasta file containing DNA sequences e.g. declare -a tri=(AAA AAC AAG AAT CAA .. etc) for i in ${tri[@]} do ...
7
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4answers
1k views

How to merge two files with different number of rows in shell?

I have file1 like this: CHR SNP TEST A1 A2 GENO O(HET) E(HET) P 0 AFFX-SNP-000541 ALL 0 0 0/0/0 ...
-2
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3answers
118 views

Deleting Lines, which match a particular Identifier from another file

I have 2 files. File 1, has an identifier (eg. D7MHBF:11:1449:1988) and every new entry starts with @. It has few more fields, which are not important in our analysis. File 2 consists of a column of ...
1
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2answers
247 views

multiple conversion bam to bed using bedtools

I have ten .bam files (bioinformatic format) and I would like to convert it to 10 .bed files, but for this conversion I need to use special command bedtools bamTobed -i (input file) > output ...
1
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4answers
4k views

Finding out the common lines in two files using 4 fields using awk and UNIX

I have 2 files. If field 1, 2, 4 and 5 of both file1 and file2 matches, then I want to print the whole line of file1 and file2 one after another in my output file. File1: sc2/80 20 . ...
11
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1answer
21k views

Best Linux Distribution for Scientific Computing? [closed]

I recently bought a new laptop to be used for scientific research when I'm at home. The machine has Intel i7 processor with 8 cores, 4 GB of RAM, and a graphic card from Nvidia (2 GB, Ivy Bridge). The ...
1
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1answer
118 views

How do I reinstall the bioperl modules on Ubuntu?

I am trying to learn bioinformatics the hard way. I have no background in Linux, Ubuntu, bash, Perl, Python, etc. I'm trying to use several programs, mostly the bioperl modules, that have been ...
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2answers
428 views

Linux Distribution for bioinformatics?

I need a linux distro which is designed for bioinformatics including some bioinformatics tool, a sample database, etc.