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Search: Posts Made By: roshanbernard
Forum: General 06-06-2015, 12:25 AM
Replies: 1
Views: 2,313
Posted By roshanbernard
i was bit early in posting this..:).. found a...

i was bit early in posting this..:).. found a solution myself... if anyone needs this info...

Go to this website

http://www.webact.org/WebACT/generate

upload ur sequences... and in a while...
Forum: General 06-05-2015, 11:35 PM
Replies: 1
Views: 2,313
Posted By roshanbernard
Help in ACT(artemis) comparision tool

Hi,

i have three whole genome sequence from bacteria and i want to compare them. I am trying to Use ACT from artemis for the comparison. While i am trying to upload the files it is prompting me to...
Forum: Sample Prep / Library Generation 04-14-2015, 05:17 PM
Replies: 2
Views: 1,444
Posted By roshanbernard
Reducing contamination in 16s PCR for metagenomic library prer

Hi everybody,

Recently i came across with the contamination with he PCR kits while i was trying to amplify the 16s Amplicons using V1-V2 primers. i have used Takara and Bioneer kits. But both of...
Forum: Bioinformatics 01-13-2015, 04:44 PM
Replies: 0
Views: 930
Posted By roshanbernard
Draing the WGS mapping

Hi,

I wanna draw a circular genomic map of the bacterial DNA. Unfortunately i have contigs only. Is there any software where i can compare the contigs into reference(circular bacterial DNA) and...
Forum: Bioinformatics 09-25-2014, 11:33 PM
Replies: 0
Views: 990
Posted By roshanbernard
Hardware requirement for Meta genomics analysis

Hi guys,

We are planning to perform a meta-genomic analysis using Iontorrent 16s amplicon sequencing.

However, i would like to know what is the decent configuration for the Computer hardware......
Forum: Bioinformatics 01-10-2014, 11:15 PM
Replies: 0
Views: 1,105
Posted By roshanbernard
Whole genome alighment and comparision

Hi,

Needed some advice one whole genome alignment.

I use Mauve for alignment. However when i use the Mauve contig mover it arranges the LCB's similar to reference LCB's....

can anyone tell...
Forum: Bioinformatics 12-19-2013, 10:59 PM
Replies: 7
Views: 2,236
Posted By roshanbernard
Yes exactly... thats the problem.. i dont know...

Yes exactly... thats the problem.. i dont know why this is happening..
Forum: Bioinformatics 12-19-2013, 04:44 PM
Replies: 7
Views: 2,236
Posted By roshanbernard
Yeah exactly.... its the same 903bp... same...

Yeah exactly.... its the same 903bp... same nucleotides but the annotation is different... so i am wondering...

thanks
Forum: Bioinformatics 12-19-2013, 03:58 AM
Replies: 7
Views: 2,236
Posted By roshanbernard
Thanks for your reply... when i checked the...

Thanks for your reply...

when i checked the WGS and there is a gene which is 903bp on two different contigs of same genome. But the annotations are given below for each
...
Forum: Bioinformatics 12-18-2013, 09:42 PM
Replies: 7
Views: 2,236
Posted By roshanbernard
Help with annotations

Hi,

I have WGS of Bacteria.

However when i cross checked the annotation done by RAST-SEED server.

i can see some errors.

Same nucleotides have been given different annotation names.
Forum: Bioinformatics 11-11-2013, 11:41 PM
Replies: 4
Views: 1,093
Posted By roshanbernard
thank you.. :)

thank you.. :)
Forum: Bioinformatics 11-11-2013, 11:20 PM
Replies: 4
Views: 1,093
Posted By roshanbernard
Thanks a lot for the reply., Can i do it...

Thanks a lot for the reply.,

Can i do it even if its a set of contigs. i have around 70 contigs in each genome
Forum: Bioinformatics 11-11-2013, 08:25 PM
Replies: 4
Views: 1,093
Posted By roshanbernard
Whole genome alighment

Hi,

Can someone suggest me the tools which can be used for whole genome alignments.

I am having the data in contigs and not as one complete circular genome.

and i need to compare two...
Forum: Ion Torrent 07-01-2013, 04:24 PM
Replies: 7
Views: 6,382
Posted By roshanbernard
thanks a lot jonathan. Our preference was to save...

thanks a lot jonathan. Our preference was to save money. we are not interested in gap filling and stuff. we were looking for some specific genes. we have 84 bacterial samples for sequencing. Ur info...
Forum: Ion Torrent 06-26-2013, 07:07 PM
Replies: 7
Views: 6,382
Posted By roshanbernard
My boss is interested in ion torrent.. because we...

My boss is interested in ion torrent.. because we have got that machine in our institute.. however yesterday we spoke to applied biosciances, they said they are gonna use 318chips with 100X...
Forum: Ion Torrent 06-25-2013, 03:47 PM
Replies: 7
Views: 6,382
Posted By roshanbernard
ah okie... previously we have used the illumina...

ah okie... previously we have used the illumina reads. this is the first time we are going with ion torrent. anyways lets hope for the best.. i am planning to go with 35 to 40X... thanks a lot..
Forum: Illumina/Solexa 06-25-2013, 03:44 PM
Replies: 4
Views: 2,214
Posted By roshanbernard
Thanks a lot for the info... :)

Thanks a lot for the info... :)
Forum: Illumina/Solexa 06-25-2013, 07:03 AM
Replies: 4
Views: 2,214
Posted By roshanbernard
Hi, i am having same concern. though i am...

Hi,

i am having same concern. though i am using Ion torrent for the same. Any idea what is the ideal coverage i need to maintain to get the accurate results...

if u come across any info, please...
Forum: Ion Torrent 06-25-2013, 06:20 AM
Replies: 7
Views: 6,382
Posted By roshanbernard
Ion torrent: bacterial WGS coverage

Hi all,

I am new to ion torrent.

We are interested in getting the bacterial whole genome sequencing( ~2MB )...

However, i am not sure what is the coverage/depth we need to use to get the...
Forum: Bioinformatics 01-18-2012, 11:14 PM
Replies: 3
Views: 1,790
Posted By roshanbernard
and thanks a lot masha for ur reply..:-)..

and thanks a lot masha for ur reply..:-)..
Forum: Bioinformatics 01-18-2012, 11:14 PM
Replies: 3
Views: 1,790
Posted By roshanbernard
Hi, i got the reply from RAST team///i am...

Hi,

i got the reply from RAST team///i am pasting the reply below....


Unfortunately, the only type of promoter sites RAST can recognize
are Ribosomal Binding Sites. RAST cannot yet...
Forum: Bioinformatics 01-18-2012, 05:39 PM
Replies: 3
Views: 1,790
Posted By roshanbernard
annotations

I use annotations pipelines like RAST or NCBI or JGI to get the bacterial genome annotation...


however, if there is any mutation among the promoter of the gene, does the servers annotated them...
Forum: Bioinformatics 01-18-2012, 05:28 PM
Replies: 1
Views: 1,343
Posted By roshanbernard
Also one more question.... However, However,...

Also one more question....

However, However, i have a query about annotation. I have two WGS, one mutant and other wild type.....
while performing the annotation, if there is any mutation in the...
Forum: Bioinformatics 01-17-2012, 04:13 PM
Replies: 1
Views: 1,343
Posted By roshanbernard
annotations intervals problem

Hi guys,

I have two whole genome sequence pf bacteria, mutant and wild type.

I got this annotates in RAST server. and when i try to compare any specific gene and gene product....there is some...
Forum: Bioinformatics 12-16-2011, 03:31 PM
Replies: 5
Views: 3,279
Posted By roshanbernard
thanks everybody...i will check CSHL and sign up...

thanks everybody...i will check CSHL and sign up on the aboe mail list...
Showing results 1 to 25 of 31

 


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