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Search: Posts Made By: Rao
Forum: Bioinformatics 01-21-2011, 03:11 AM
Replies: 1
Views: 2,554
Posted By Rao
Use GFF3 format

Use GFF3 format
Forum: Service Providers 01-21-2011, 02:59 AM
Replies: 14
Views: 8,843
Posted By Rao
Ocimum Biosolutions, India...

Ocimum Biosolutions, India (http://www3.ocimumbio.com/)
Forum: Bioinformatics 06-21-2010, 07:03 AM
Replies: 11
Views: 10,279
Posted By Rao
try with bowtie... is it RNA-seq data?

try with bowtie...
is it RNA-seq data?
Forum: Bioinformatics 06-21-2010, 06:58 AM
Replies: 15
Views: 5,974
Posted By Rao
try samtools pileup -vcf gives only varients

try samtools pileup -vcf
gives only varients
Forum: SOLiD 06-16-2010, 11:06 PM
Replies: 6
Views: 3,080
Posted By Rao
data set is available on...

data set is available on solidsoftwarecommunity.com
Forum: Bioinformatics 06-16-2010, 11:04 PM
Replies: 5
Views: 2,609
Posted By Rao
mummer may be best option

mummer may be best option
Forum: Bioinformatics 06-16-2010, 11:01 PM
Replies: 15
Views: 5,974
Posted By Rao
You can try VarScan...takes pileup as input

You can try VarScan...takes pileup as input
Forum: Epigenetics 01-11-2010, 05:19 AM
Replies: 12
Views: 4,883
Posted By Rao
Chiper, If you see this paper at...

Chiper,

If you see this paper at http://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.1371.html, says three kinds of peaks, may give some idea about long peaks...

Classes of ChIP-seq signals....
Forum: Bioinformatics 01-05-2010, 02:17 AM
Replies: 24
Views: 7,462
Posted By Rao
You can try velvet assembler... it accepts both...

You can try velvet assembler... it accepts both long and short reads
Forum: Epigenetics 12-29-2009, 11:23 PM
Replies: 12
Views: 4,883
Posted By Rao
I would suggest upload peaks and the reads that...

I would suggest upload peaks and the reads that are responsible for these peaks to any genome browser. Compare the results and the distribution of reads in the peaks region. This may give a better...
Forum: General 12-23-2009, 12:46 AM
Replies: 13
Views: 8,181
Posted By Rao
from ucsc genome browser...

from ucsc genome browser...
Forum: Bioinformatics 12-23-2009, 12:37 AM
Replies: 11
Views: 4,837
Posted By Rao
based on genome size... i think it decides k-mer...

based on genome size... i think it decides k-mer size that used for error correction
Forum: Bioinformatics 08-24-2009, 10:45 PM
Replies: 3
Views: 1,712
Posted By Rao
there are some gaps (are represented in Ns)

there are some gaps (are represented in Ns)
Forum: Introductions 08-19-2009, 05:33 AM
Replies: 2
Views: 1,684
Posted By Rao
"repetitive elements"... what kind of...

"repetitive elements"... what kind of repeats?
Forum: SOLiD 07-07-2009, 08:36 PM
Replies: 14
Views: 3,645
Posted By Rao
Also there compiled MaToGff tool available from...

Also there compiled MaToGff tool available from the same site
Forum: SOLiD 07-07-2009, 08:35 PM
Replies: 14
Views: 3,645
Posted By Rao
I think you are using RNA pipeline... there is a...

I think you are using RNA pipeline... there is a option to generate GFF files
Forum: Bioinformatics 06-28-2009, 08:44 PM
Replies: 25
Views: 13,726
Posted By Rao
Thanks for the update...

Thanks for the update...
Forum: SOLiD 06-15-2009, 08:57 PM
Replies: 2
Views: 1,900
Posted By Rao
You will get them from NCBI databases, and...

You will get them from NCBI databases, and adapter sequences ..get them from vendor...(may from some documentation)...
Forum: Bioinformatics 06-10-2009, 08:58 PM
Replies: 25
Views: 13,726
Posted By Rao
Hash length is overlap b/w reads (based on this...

Hash length is overlap b/w reads (based on this it makes graph).... if it more you get better assembly....if you keep less, there is a chance of mis-assemblies....I think maximum you can keep 31 (it...
Forum: De novo discovery 04-28-2009, 01:02 AM
Replies: 82
Views: 43,359
Posted By Rao
Check for ESTs may help you in assembly de novo...

Check for ESTs may help you in assembly
de novo assembly of transcriptome.... what about misassemblies...
Forum: De novo discovery 04-22-2009, 02:40 AM
Replies: 18
Views: 7,133
Posted By Rao
http://www.cs.sunysb.edu/~skiena/shorty/ SHORTY...

http://www.cs.sunysb.edu/~skiena/shorty/
SHORTY
What is the status this tool...?
Forum: 454 Pyrosequencing 04-08-2009, 09:49 PM
Replies: 2
Views: 2,510
Posted By Rao
I hope it will help you... ...

I hope it will help you...

http://seqanswers.com/forums/showthread.php?t=948&highlight=service
(List of Next Gen Sequencing Service Providers)
Forum: SOLiD 03-26-2009, 09:01 PM
Replies: 35
Views: 20,229
Posted By Rao
You mean converting colorspace seq.. to basespace...

You mean converting colorspace seq.. to basespace seq...
Forum: Bioinformatics 03-22-2009, 09:26 PM
Replies: 16
Views: 3,816
Posted By Rao
I've no idea about consed... but we can use...

I've no idea about consed... but we can use BioPerl for this...
see this link for more on this... http://www.bioperl.org/wiki/Module:Bio::SeqIO
Forum: 454 Pyrosequencing 03-18-2009, 08:52 PM
Replies: 2
Views: 1,382
Posted By Rao
short read mate-pair may help you to fill the...

short read mate-pair may help you to fill the gaps...
Below link may help you...
De Novo plant Bac sequencing (http://seqanswers.com/forums/showthread.php?t=1179)
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