BOL: All site questions

How MIRA follows for the ref based assembly?

Neel — Fri, 08 Jul 2016 07:15:26 -0500

MIRA follows for the ref based assembly (like mapping the reads on the reference with xxx, etc.) and if its possible to have a figure with the workflow.

Is there any job offers in Bioinformatics?

Geetanjali Rajput — Sun, 03 Jul 2016 15:07:57 -0500

Hi BOL community,

I, Geetanjali, recently completed Msc in bioinformatics. I would like to know more about job offers in Bioinformatics.

Please help.

Quick way to calculate length of multiple fasta file!!

Anjana — Thu, 30 Jun 2016 10:49:12 -0500

I am using this perl code right nowadays.

#!/usr/bin/perl
use warnings;
use strict;
open(FASTA, "<", seq.fa) or die("Can't open\n");
my %singleLineSequences;
my $sequence_id;
while(){
    my $line = $_; chomp($line);
    if ($line =~ m/^>(\S+)/){
        $sequence_id = $1;  
        $singleLineSequences{$sequence_id} = ""; 
        }
    else {
        $singleLineSequences{$sequence_id} = $singleLineSequences{$sequence_id} . $line;
        }
   }


foreach my $sequence_entry (keys %singleLineSequences){
    my $currentSequence = $singleLineSequences{$sequence_entry};
    my $lengthSequence = length($currentSequence);
    print $sequence_entry . "," . $lengthSequence . "\n";
}

Need help in Blastn?

Shruti Paniwala — Mon, 20 Jun 2016 08:13:32 -0500

I am doing megablast of a contig against NR database, but unable to understand this

-outfmt '6 qseqid staxids qstart qend sstart send qseq sseq evalue length'

Can you please help me to undestand all these.

How to change the file path for Linux to Window in Perl?

Aasha — Thu, 09 Jun 2016 05:39:42 -0500

In which journals should I publish my bioinformatics software/tools?

Nishi Singh — Wed, 25 May 2016 05:08:25 -0500

Until there is a radical change in the way that academic credit is given, the principal record of scientific research is still the peer-reviewed publication. Given that software is a fundamental part of doing science in the digital age, the question we are often asked is: where can I publish papers which are primarily focused on my scientific software?

RNAseq dataset for different cancers stages !!

Anjana — Sun, 01 May 2016 19:24:04 -0500

Is there any database exists which provides RNAseq data for different cancers stages?

GLIBC_2.14 error with SatsumaSynteny !!

Jit — Wed, 06 Apr 2016 14:13:55 -0500

I run SatsumaSynteny on my server using following command:

[jit@hm satsuma-code-0]$ ./SatsumaSynteny -q Genome/renamedG.fa -t Genome/genome_v4.fasta -o Genome/OutFile -m 128 -ni 10 -n 256 -chain_only

But it kill the program with followng error:

./SatsumaSynteny: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./SatsumaSynteny)

Can anyone please help to resolve this.

My server detail:

[jit@hm satsuma-code-0]$ lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 12
On-line CPU(s) list: 0-11
Thread(s) per core: 1
Core(s) per socket: 6
Socket(s): 2
NUMA node(s): 2
Vendor ID: AuthenticAMD
CPU family: 16
Model: 8
Stepping: 1
CPU MHz: 2600.186
BogoMIPS: 5200.03
Virtualization: AMD-V
L1d cache: 64K
L1i cache: 64K
L2 cache: 512K
L3 cache: 5118K
NUMA node0 CPU(s): 0,2-6
NUMA node1 CPU(s): 1,7-11

Human chromosome length extractor !

Priya Singh — Fri, 25 Mar 2016 12:42:39 -0500

Is there any easiest known way to extract organism's chromosome length?

How to count the occurance of letters in fasta file?

Poonam Mahapatra — Wed, 23 Mar 2016 09:14:23 -0500

I received a new genome to annotated. I need your help to quickly count the occurance of all the letters in fasta file.