Hello SEQanswers Community,
I am currently facing issues with running the Variant Effect Predictor (VEP) and vcf2maf in a Conda environment...
76 results in 0.0028 seconds.
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Trouble Running VEP in Conda Environment Due to Perl DBD::mysql Error
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Module is not installing in cpan in local path
Hi,
I am trying to install Getopt::Long::Subcommand module on my account on a cluster local folder on cpan. First i set the local path to...Last edited by amitbik; 03-02-2021, 07:53 AM. -
Script to calculate Dipeptide composition
Hi all, I would like to use a script (python, shell, or perl) to calculate the percentages of dipeptide composition from multiple protein sequences (fasta... -
How to start a new column after every nth row?
Hi have a file(comma separated) with 3 columns. I want to start new column after every 4th row
Input:
col1,col2,col3
1,disease1,high... -
Failed connection with Ensembl VEP script on port 3337
I'm using the VEP (Variant Effect Predictor) standalone Perl script to annotate some variants, it connects to the Ensembl MySql database. I used the same... -
Parsing Blast xml using Perl (BioPerl)
Hi people,
I'd like to resolve the following problem(s):
I'm trying to resolve the structure of reads, partial of retroviral origin,... -
Provlems running VelvetOptimiser
Hi everyone,
When trying to run VelvetOptimiser.pl from the VelvetOptimiser-master directory, (downloaded from: https://github.com/tse... -
Generating limited amount of random numbers in Perl for a known range
Hi!
I am a newbie in here and wanted to ask a question that I am not able to find its answer. I have a file which has couple letters as :... -
Perl Task
Hey everybody, I'm new here. Currently I've been teaching myself (biology student) how to use part, in particular for sequence alignments. Now I'm trying... -
How do I convert one file into several multifasta fasta files using perl
Hi
It's the first time I work with Perl then I don't know so much about the language.
I need a script which converts multi-fasta file in several...Last edited by iMarcelo; 05-05-2016, 10:25 AM. -
Installation of rnammer-1.2 for Trinnoate: which version Perl XML/Simple.pm is requir
Hi Trinity community,
I am working on step 6. Running RNAMMER to identify rRNA transcripts of the Trinoate protocol detailed on https://... -
Prinseq-lite problem
Dear all,
I am using prinseq (v.0.20.4, CentOS) to filter my paried end data with the following commands.
[root@localhost]# perl prinseq-lite.pl...Last edited by kumar03; 12-09-2015, 06:40 PM. -
How to tell legacy_blast.pl to look for blastp in different path?
Hello,
I was testing pantherScore.pl but then I got this :
Can't exec "/usr/bin/blastp": No such file or directory at... -
Anyone knows where to find FamLibBuilder module? (necessary for pantherScore.pl)
Hey everyone, I was trying to use PANTHER (http://www.pantherdb.org/) on my RNA-seq dataset.
However, as I tried to generate the panther ID, i... -
Script To Calculate Word Frequency For Many Sequences
Hello!
Who can help me with a writing a script?
1. For each file in the set (archive, probably):
Open input...
