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Forum: Genomic Resequencing 11-18-2013, 10:52 PM
Replies: 0
Views: 2,580
Posted By sivasubramani
CNS file format

Hi

I got a set of file names as **.cns I am sure this contains ref and var bases along with some quality values. Please help me out to understand what all the headers.

chromosome_7 1 A...
Forum: Bioinformatics 09-29-2013, 11:17 PM
Replies: 1
Views: 2,516
Posted By sivasubramani
cd-hit output clarification

Hi all,

I got an output from cd-hit-est as follows.
>Cluster 1
0 1997nt, >Locus_3753_Transcript_3/6_Confidence_0.182_Length_1997_UP10_UP11... at 208:1784:3900:5486/+/92.67%
1 ...
Forum: Bioinformatics 09-29-2013, 11:16 PM
Replies: 9
Views: 4,547
Posted By sivasubramani
Hi all, I got an output from cd-hit-est as...

Hi all,

I got an output from cd-hit-est as follows.
>Cluster 1
0 1997nt, >Locus_3753_Transcript_3/6_Confidence_0.182_Length_1997_UP10_UP11... at 208:1784:3900:5486/+/92.67%
1 ...
Forum: Bioinformatics 07-29-2013, 01:56 AM
Replies: 5
Views: 3,156
Posted By sivasubramani
Dear All, I was trying to use PAGIT - Post...

Dear All,

I was trying to use PAGIT - Post Assembly Genome Improvement Toolkit, for one of my assembly. I could not find any proper manual to explaing the steps. when I opened the dotestrun.sh...
Forum: Bioinformatics 07-29-2013, 01:54 AM
Replies: 1
Views: 1,371
Posted By sivasubramani
PAGIT input files

Dear All,

I was trying to use PAGIT - Post Assembly Genome Improvement Toolkit, for one of my assembly. I could not find any proper manual to explaing the steps. when I opened the dotestrun.sh...
Forum: Bioinformatics 07-24-2013, 11:02 PM
Replies: 5
Views: 4,017
Posted By sivasubramani
Hope you got the answer..:)

Hope you got the answer..:)
Forum: Bioinformatics 07-23-2013, 09:02 PM
Replies: 19
Views: 3,231
Posted By sivasubramani
In HHblits package, there is a script which does...

In HHblits package, there is a script which does the way you want.

HHblits_src/scripts/splitfasta.pl
Forum: De novo discovery 05-28-2013, 08:52 AM
Replies: 2
Views: 1,640
Posted By sivasubramani
try minia... fast and memory efficient.. ...

try minia... fast and memory efficient..

Good luck..
Forum: Illumina/Solexa 05-28-2013, 08:42 AM
Replies: 4
Views: 1,716
Posted By sivasubramani
fermi, minia.. these will work fast also takes...

fermi, minia.. these will work fast also takes less memory.. Velvet, SOAP denovo are like super stars in assembly, MIRA would be better if you have sooooo much patiance...

Good luck
Forum: Bioinformatics 04-09-2013, 11:04 PM
Replies: 10
Views: 3,629
Posted By sivasubramani
Hey all, I am looking for the transcripts...

Hey all,

I am looking for the transcripts which are extended or clipped in either 5' or 3' end. Could anyone help me with this..?? What classcode would be helpful in understanding this...
Forum: De novo discovery 04-01-2013, 02:29 AM
Replies: 15
Views: 5,957
Posted By sivasubramani
Hello Rayanc, I appreciate the work what you...

Hello Rayanc,

I appreciate the work what you have done on minia. If you can mention about the platform on what we can use minia (illumina or SOLiD, etc) also it can handle colorspace data..??
...
Forum: Bioinformatics 04-01-2013, 02:18 AM
Replies: 13
Views: 5,772
Posted By sivasubramani
Hello waterboy, What is the assembly tool...

Hello waterboy,

What is the assembly tool you used to assemble SOLiD MP data...??

Thanks,
Forum: Bioinformatics 02-26-2013, 01:20 AM
Replies: 17
Views: 8,723
Posted By sivasubramani
I just completed reading the first(parent) post....

I just completed reading the first(parent) post. There I got some doubts and where the data could have gone in different direction.
1. What is the kmer length you used for assembly. Becuase in such...
Forum: Introductions 08-26-2011, 02:02 AM
Replies: 1
Views: 2,105
Posted By sivasubramani
Rank In Soap denovo

Dear all,
I am trying to use soap denovo tool for my large data assembly.
I have some doubts regarding that..

what is rank in config file
can we run multiple Kmers in a single run..??
...
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