User: zubenel

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zubenel110
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Posts by zubenel

<prev • 22 results • page 1 of 3 • next >
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Answer: A: Retrieving 16s rRNA from Whole genome sequence using PERL
... For learning Perl in general you may look at books mentioned [here][1] or [tutorial][2]. Bioinformatics related books are old but can be useful as this [one][3] has a chapter on parsing Genbank data. In addition to this you may look at BioPerl [documentation][4]. For your case I created small scrip ...
written 4 months ago by zubenel110
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Answer: A: How to split sequence in fasta file based on long runs of Ns?
... If you install [bioperl][1] module Bio::SeqIO you could use the script below. Just save it as split_fasta.pl and run like `./split_fasta input.fasta output.fasta 100`. In this way sequences from input.fasta file will be divided by 100 Ns and saved to file output.fasta. If the sequence called "s ...
written 8 months ago by zubenel110
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Answer: A: Remove contigs that are lower than 200
... You can perform this task if you install [BioPerl module Bio::SeqIO][1]. Then you can save the script below as filter_contigs.pl in the same directory as file with contigs and run the script with `perl filter_contigs.pl`. It will remove contigs that are shorter than 200 bp from input file **contigs. ...
written 8 months ago by zubenel110
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Answer: A: Converting Illumina fastq quality scores to phred
... Assuming phred+33 another easy solution is to use Perl oneliner like this: `perl -E 'say ord("A")-33'` ...
written 9 months ago by zubenel110
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Comment: C: there is error when i use CPAN install perl model
... I suggest to ask this question on one of these sites: [r/perl][1] or [stackoverflow][2] with tag [perl] or [perlmonks][3]. There will be more people that could help. [1]: http://www.reddit.com/r/perl/ [2]: http://stackoverflow.com/ [3]: http://perlmonks.org/ ...
written 10 months ago by zubenel110
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Comment: C: Want to edit bioperl script for making .ptt files (for each contig) from .gbk fi
... Let's say your file is called `seqs.gbk` and is in the same folder as Perl script. All you need to do is to change the line: my $gbk = Bio::SeqIO->new(-fh=>\*STDIN, -format=>'genbank'); to this: my $gbk = Bio::SeqIO->new(-file=>'seqs.gbk', -format=>'genbank'); By doing ...
written 10 months ago by zubenel110
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Answer: A: Does miRDeep2.pl module support multi-thread?
... You are right as there is no option for running miRDeep2.pl by enabling multithreading. If you know Perl well enough you could study miRDeep2.pl script in order to find out if it is worth it to try incorporate multithreading. If you follow this route you may find [Perl tutorial on threads][1] useful ...
written 10 months ago by zubenel110
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Comment: C: miRDeep2- mapper problem with perl install.pl installation?
... From the code you have given it seems that you try to run a script in a wrong folder: ~/Desktop/SmallRNAseqdata. What is the output on terminal after you run these commands: $ cd /home/harshraj/mirdeep2_pa $ perl install.pl Have you tried to run `mapper.pl` after these 2 commands? In case ...
written 10 months ago by zubenel110
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Answer: A: Interactive Perl Learning
... Previously mentioned [Perltuts][1] do work as of today. Alternative interactive resource that might be useful is [tryperl.pl][2] [1]: http://www.perltuts.com/ [2]: https://tryperl.pl/ ...
written 10 months ago by zubenel110
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Comment: C: Want to edit bioperl script for making .ptt files (for each contig) from .gbk fi
... Does Padre show any error message? In any case you should use `#!/usr/bin/env perl` instead of `!/usr/bin/env perl`. And error with `use Bio::SeqIO` could be because this module is not installed. You can install it by opening **CPAN client** from start menu and running these commands: get Bio:: ...
written 10 months ago by zubenel110

Latest awards to zubenel

Supporter 7 months ago, voted at least 25 times.
Scholar 8 months ago, created an answer that has been accepted. For A: Remove contigs that are lower than 200
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Remove contigs that are lower than 200
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Error indexing genome with STAR

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