BOL

Hi BOL community,

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

Please help.

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";
}

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.

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?

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

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

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

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

i have downloaded sra file and converted into paired end FastQ having following headers:

@HWUSI-EAS754_0001:4:1:5605:1034#GCCAT

The head and tail of file are as follow

Head:

==> ERR042057_1.fastq <==
@HWUSI-EAS754_0001:4:1:5605:1034#GCCAAT
TNACTGTTTCTCTAAAACCTTACAAGAAAAACTAAGCTTCTCTAAACTTGTATTCATTATGGGAGNATGNCA
+HWUSI-EAS754_0001:4:1:5605:1034#GCCAAT
C)CCCGGGGGIIIIIIIIIIIIIHIIIIIIIIIIIGIHIIIIIHHIIIHIHIIHIIHIIHAAA?B#######
@HWUSI-EAS754_0001:4:1:6122:1035#GCCAAT
ANGTTGTCTAAAGTAATAACTCCATTGGCTATTATTTTCTAAACATCTAAAACAAAACTTAACTANCGANAT
+HWUSI-EAS754_0001:4:1:6122:1035#GCCAAT
B(B?BGGGGGIIIICIIIIIIIIIIIIIIIIHIHIIIIIIIIIIIIGIIIIIIFIIIIGIEEECE#######
@HWUSI-EAS754_0001:4:1:6654:1035#GCCAAT
TNTTTAAATAAAAGGTTCTGTATCTTGATCCTGAAGTATCCTGTAATAGCCTACAGTGAAAAGAANACANTT

==> ERR042057_2.fastq <==
@HWUSI-EAS754_0001:4:1:5605:1034#GCCAAT
AAGAAATTTATTCCTGCAGATCAATATTTCCCGCAACCACTTGAGAATTTCTGTGCTACTAAGCATTTGATG
+HWUSI-EAS754_0001:4:1:5605:1034#GCCAAT
IIHHHIIIIHIHIIHGIIIIIIGIHGGG4D<??:@CC?C@CGEDFGEEEEGH>EH<BEEFED8CFBEBEB?#
@HWUSI-EAS754_0001:4:1:6122:1035#GCCAAT
AGAAACTGAGCTGAAGAGGGTAAAAGTCCTTGGCTCAGGTGCTTTTGGAACGGTTTATAAAGTAAGTAAAAA
+HWUSI-EAS754_0001:4:1:6122:1035#GCCAAT
HHGHHHHHHHHHHHHHFHHHHHHFFHEHHHGHGH<DBDB=DDDDDBFCDEB><BB>CBDB=D?BE?8A?A37
@HWUSI-EAS754_0001:4:1:6654:1035#GCCAAT
CTAAACCCCCCCCCACCCCACCCCCCCACCACACCAACCCCACCCACACACCCCAACCACCCTCACACTCTC



Tail:

==> ERR042057_1.fastq <==
+HWUSI-EAS754_0001:4:120:19005:21176#GCCAAT
G>D>DBDDGBGGE@>EGGGGBG;GGGGDBG##########################################
@HWUSI-EAS754_0001:4:120:19024:21176#GCCAAT
GAGAAAGAATTCAAACTGATTTTTCTTTTCTTNNNNNNNNNNNNGGGCACTNNNNNNNNNNNTGGCCCTCCT
+HWUSI-EAS754_0001:4:120:19024:21176#GCCAAT
IIIEIIIHIIIHIIIIIIEIHIIIIHHIII##########################################
@HWUSI-EAS754_0001:4:120:19130:21175#GCCAAT
CGGGGAAGAGCGCCAGCACCGAGGTGCCAGGTNNNNNNNNNNNNGCGGAGAANNNNNNNNNNATCATGCAGT
+HWUSI-EAS754_0001:4:120:19130:21175#GCCAAT
HIGIIHIIIIIIIHDIIHIIGGII@DD?BD##########################################

==> ERR042057_2.fastq <==
+HWUSI-EAS754_0001:4:120:19005:21176#GCCAAT
?AA6A?A?A?A@@<A#########################################################
@HWUSI-EAS754_0001:4:120:19024:21176#GCCAAT
ATTAGCAGACATATATCTTTTCTCTGAAATCTAAATACTTGCAGAAATACTAATTTTCATTTTATATTATGT
+HWUSI-EAS754_0001:4:120:19024:21176#GCCAAT
HGHHFFEHEHHHFHHBDBH:DGGGEHFBHHHDGHHHDHDHBGGGEGGEGGGBGGG(+:;;F<=F@;FE?EGG
@HWUSI-EAS754_0001:4:120:19130:21175#GCCAAT
CAAAGCAGGCCCCACGAGGCTGGCTGCGTGCGGGGTGCTCACCCGTGGCCGGTCCTGCGGGGCCCGCTGATC
+HWUSI-EAS754_0001:4:120:19130:21175#GCCAAT
HFHHHHHHEHHHHHHA3E8GD>GGBBEEBEGG<G>?AD>GGGEEGD>G@DGD3D##################

How to determine the @RG ?

I'm using the following command to add @RG tag:

java -jar picard.jar AddOrReplaceReadGroups I=input.bam O=output.bam RGID=? RGLB=? RGPL=illumina RGPU=? RGSM=?

What should be the @RG tags values for following parameters:

RGID=?

RGLB=?

RGPL=illumina

RGPU=?

RGSM=?

The link for SRA data is :

http://www.ncbi.nlm.nih.gov/sra/ERX019190[accn

Thankyou in advance