User: zubenel

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zubenel10
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Posts by zubenel

<prev • 18 results • page 1 of 2 • next >
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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 3 days ago by zubenel10
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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 6 days ago by zubenel10
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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 7 days ago by zubenel10
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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 7 days ago by zubenel10
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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 8 days ago by zubenel10
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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 16 days ago by zubenel10
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Answer: A: How to extract 3', 5' UTR sequences from genbank records using python, PERL and
... If you have gff file you might try to use [gff2fasta.pl][1] with option -feature set as "five_prime_UTR" or "three_prime_UTR" or something like that. Also you may read how to get sequences of specific features with [BioPerl][2]. [1]: https://github.com/minillinim/gff2fasta [2]: https://bioperl ...
written 21 days ago by zubenel10
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Comment: C: Can't get known motif enrichment result using findMotifs.pl (Homer)
... It seems that there is something wrong with gene id conversion. You may try this: use input file with gene names in `TAIR` format and add option `-noconvert`. In this way ids will not be converted. I ran analysis with small list of randomly chosen genes: AT3G44150 AT4G36350 AT5G48910 ...
written 24 days ago by zubenel10
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Comment: C: Setting FDR at 0.05
... By applying filter `which(res_HIGADOvsPULMON$padj < 0.05)` you have removed all the cases where adjusted p-values >= 0.05 and that includes all the cases where p-value is between 0.05 and 0.1. If you want to compare `summary` results you have to use unfiltered `res_HIGADOvsPULMON` object. ...
written 4 weeks ago by zubenel10
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Answer: A: Setting FDR at 0.05
... DESeq2 summary function has two main arguments: `object` and `alpha` which means the adjusted p-value cutoff. To change cutoff you need to change alpha argument value. For example: summary(object = res, alpha = 0.05) Or shorter version without writing argument names: summary(res, 0.05) ...
written 4 weeks ago by zubenel10

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Popular Question 2.4 years ago, created a question with more than 1,000 views. For Error indexing genome with STAR

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