BOL

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

Iam searching for the exome data for an eye disease "Glaucoma" obtained by next generation sequencing platform but unfortunately  i am not able to get that data. I have already searched ncbi SRC, GEO data sets of ncbi but no data is available. Is there any database other than these to get data in FASTQC format?? Or any article related to glaucoma where information about datasets is available.

thanks

There are many mapping tools, and each one has its own specifications. Once we have two or more tools for similar purposes, how can we say which tool is better?