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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3
votes
2answers
75 views

Organizing three dimensional data with awk/sed/perl

I have this file (a sparse matrix): PC.354 OTU1 6 PC.354 OTU2 1 PC.356 OTU0 4 PC.356 OTU2 7 PC.356 OTU3 3 I want an output like this (dense matrix -classic .biom table): OTU_ID PC.354 PC.355 ...
2
votes
0answers
18 views

How do I blastp multiple fasta files, and move the files with say 50 to 90% similarity to another folder?

So I have about 100 fasta files to blast and I need to find files with 50 to 90% similarities with the database file. Then the files are to be moved to a new folder. How do I do this?
1
vote
1answer
65 views

Converting column data to matrix

I am trying to create a matrix of plant traits and plant species. There are 2,912,746 rows in the data and 3 columns. There are different numbers of traits for each species, and not every species has ...
3
votes
2answers
69 views

How to sort data by the numbers in third column? [duplicate]

If I have a file consisting of data that looks as follows, how would I sort the data based on the numbers in the 3rd column ? The space between the first two columns are NOT tab delimited but some ...
0
votes
0answers
55 views

How to run a BBMap software .sh script in a for loop for a set of 100 .fasta files?

cd /home/user/Documents/bbmap ./bbmap.sh ref=fake.fa # indexes fasta format file sets ref filelist="fastaone.fasta, fastatwo.fasta, fastathree.fasta" for list in "$filelist" do ./bbmap.sh done Is ...
0
votes
0answers
13 views

Question: Running PSI-BLAST Against Multiple Queries

I'm new in standalone blast+ and in linux terminal. I set the bash-profile to load the PATH and BLASTDB for my blast already, but I don't know how to use psi-blast yet. The question is - Can I and How ...
1
vote
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 . ...
0
votes
0answers
83 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) ...
7
votes
4answers
2k 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
votes
2answers
208 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
votes
2answers
2k 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 ...
1
vote
2answers
156 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 ...
1
vote
2answers
365 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 ...
0
votes
1answer
167 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. ...
-1
votes
3answers
203 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
vote
1answer
133 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). ...
4
votes
2answers
437 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 ...
-2
votes
3answers
126 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 ...
5
votes
1answer
985 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 ...
1
vote
1answer
128 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 ...
12
votes
1answer
28k 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
vote
2answers
498 views

Linux Distribution for bioinformatics?

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