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Search: Posts Made By: newBioinfo
Forum: Core Facilities 09-20-2013, 12:41 PM
Replies: 11
Views: 4,153
Posted By newBioinfo
Thanks lac302, I checked the link and...

Thanks lac302,
I checked the link and contacted them, could you tell me if they do the nucleic acid extraction also.

Thanks!!
Forum: Core Facilities 09-18-2013, 05:29 PM
Replies: 11
Views: 4,153
Posted By newBioinfo
Hi genbio64, Could you provide us some...

Hi genbio64,
Could you provide us some details or contact info.

Thanks!!!
Forum: Core Facilities 09-17-2013, 11:27 AM
Replies: 11
Views: 4,153
Posted By newBioinfo
Thanks Francy87, We already have 16s rRNA...

Thanks Francy87,
We already have 16s rRNA data, now we want to do metagenomics and metatranscriptomics. Is you facility offering that.


Thanks!!
Forum: Core Facilities 09-17-2013, 08:20 AM
Replies: 11
Views: 4,153
Posted By newBioinfo
Thanks aarodriguezm, I have contacted them...

Thanks aarodriguezm,
I have contacted them and waiting for their reply.
Forum: Core Facilities 09-17-2013, 06:40 AM
Replies: 11
Views: 4,153
Posted By newBioinfo
Metagenomics/Metatrancriptomics Sequencing

Hello Everyone,
We have some ice samples and want to know where could we get it sequenced. We want to do metagenomics and metatranscriptomics.
Any kind of information will be highly appreciated.
...
Forum: Metagenomics 09-13-2013, 11:51 AM
Replies: 0
Views: 1,672
Posted By newBioinfo
Metagenomics/Metatrancriptomics Sequencing

Hello Everyone,
We have some ice samples and want to know where could we get it sequenced. We want to do metagenomics and metatranscriptomics.
Any kind of information will be highly...
Forum: Bioinformatics 05-20-2013, 08:52 AM
Replies: 4
Views: 1,456
Posted By newBioinfo
Thanks ppgardne, I have reads from...

Thanks ppgardne,
I have reads from sequencing and I want to align these to ribosomal database based on secondary structure. I have aligned based on sequence and want to see if aligning based on...
Forum: Bioinformatics 05-17-2013, 11:47 AM
Replies: 4
Views: 1,456
Posted By newBioinfo
Thanks ppgarnde, Can Infernal in RDP...

Thanks ppgarnde,
Can Infernal in RDP databse can do this?
Forum: Bioinformatics 05-15-2013, 01:45 PM
Replies: 4
Views: 1,456
Posted By newBioinfo
RNA secondary structure alignment

Hi All,
Is there any aligner that can align RNA based on secondary structure.



Thanks!!!
Forum: Metagenomics 04-30-2013, 09:25 AM
Replies: 5
Views: 2,011
Posted By newBioinfo
Thanks a lot!!!

Thanks a lot!!!
Forum: Metagenomics 04-29-2013, 03:21 PM
Replies: 5
Views: 2,011
Posted By newBioinfo
Thanks JackieBadger, I did some 16S rDNA...

Thanks JackieBadger,
I did some 16S rDNA sequencing from the samples collected from ice and they were preserved in ethanol. But, now I need to do metatranscriptomic for ice samples and I am...
Forum: Metagenomics 04-29-2013, 01:34 PM
Replies: 5
Views: 2,011
Posted By newBioinfo
Sample collection for metranscriptomic sequencing

Hi All,
I need to do metatranscriptomic sequencing from ice samples. I want to know how can samples be transported from the site to the lab for RNA isolation. The ice samples will be filtered...
Forum: Bioinformatics 02-12-2013, 02:09 PM
Replies: 9
Views: 2,409
Posted By newBioinfo
Thanks GenoMax, I contacted the facility and...

Thanks GenoMax,
I contacted the facility and they have provided me the data in fastq files.
Thanks for all the help.
Forum: Bioinformatics 02-12-2013, 08:01 AM
Replies: 9
Views: 2,409
Posted By newBioinfo
Thanks GenoMax, I did get the original file...

Thanks GenoMax,
I did get the original file from the facility but as I was new to the field I asked them to demultiplex it for me and got the file I showed above. So, now I have both the files...
Forum: Bioinformatics 02-11-2013, 06:27 PM
Replies: 9
Views: 2,409
Posted By newBioinfo
Thanks Kennels, The sequencing facility did...

Thanks Kennels,
The sequencing facility did it for me, and I got the demultiplexed file which is in fasta format. Also, if I do it myself which program should I use?


Thanks!!!
Forum: Bioinformatics 02-11-2013, 01:13 PM
Replies: 9
Views: 2,409
Posted By newBioinfo
Thanks GenoMax for looking into my problem. ...

Thanks GenoMax for looking into my problem.
I got demultiplexed file which looks like this:
>R.1_00001...
Forum: Bioinformatics 02-11-2013, 12:51 PM
Replies: 9
Views: 2,409
Posted By newBioinfo
submitting data to SRA

Hi,
I am trying to submit a 16s rRNA reads from Illumina on SRA. I have reached to level where it is asking me the following things:
Flowcell, Lane, Filename, md5checksum.

I have the...
Forum: Metagenomics 01-11-2013, 11:10 AM
Replies: 3
Views: 2,546
Posted By newBioinfo
Thanks a lot!!!

Thanks a lot!!!
Forum: Metagenomics 01-11-2013, 09:08 AM
Replies: 3
Views: 2,546
Posted By newBioinfo
V4 region primers

Hi Everyone,
I may be asking very basic question but I want to know what does 'H', 'V' and 'W' indicate in the reverse primer of V4 region of 16s rRNA. The primer sequence is...
Forum: Bioinformatics 10-25-2012, 09:09 AM
Replies: 2
Views: 1,224
Posted By newBioinfo
aligned and unaligned database

Hi Everyone,
I am very confused here, I am not able to get the difference between aligned and unaligned database.
Here is an example of an aligned database:
>AF515816.1...
Forum: Illumina/Solexa 10-17-2012, 02:44 PM
Replies: 13
Views: 11,656
Posted By newBioinfo
Thanks Seven, Ii would be good if they...

Thanks Seven,
Ii would be good if they demultiplex the data before sending, but in my case it is not.
Forum: Illumina/Solexa 10-17-2012, 02:42 PM
Replies: 13
Views: 11,656
Posted By newBioinfo
Thanks JackieBadger, I am planning to use...

Thanks JackieBadger,
I am planning to use QIME, so hopefully I will not encounter such issues.



Thanks for the help!!!
Forum: Illumina/Solexa 10-17-2012, 02:40 PM
Replies: 13
Views: 11,656
Posted By newBioinfo
Thanks jackieBadger, I will try it!

Thanks jackieBadger,
I will try it!
Forum: Illumina/Solexa 10-17-2012, 11:47 AM
Replies: 13
Views: 11,656
Posted By newBioinfo
Demultiplex Illumina reads

Hi Everyone,
I am kind of stuck with my Illumina data, I want to remove the barcodes from my reads. My read file looks like this
@HWI-ST1035:115:C0RG7ACXX:5:1101:1216:2040 1:N:0:...
Forum: Bioinformatics 10-04-2012, 01:10 PM
Replies: 6
Views: 1,711
Posted By newBioinfo
Fastqc:how to get a quality score for individual read

Hi Everyone,
I have a 77 million reads and I need to know the quality score of each read so that I can filter the data based on the quality score. I used Fastqc and it gives me the graph of...
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