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Forum: Bioinformatics 04-03-2018, 07:35 AM
Replies: 0
Views: 545
Posted By bio_informatics
Micro-array: Huex 1st v2

Hello,

This is first time I'm dealing with Micro-array data. I've affymetrix human exon arrays. Cases and control in total are 223.
I tried few things but kind of lost in between.

I perform...
Forum: Bioinformatics 09-01-2017, 10:46 AM
Replies: 2
Views: 1,866
Posted By bio_informatics
Doubt for primer removal: illumina

Hi All,

I was browsing online bioinformatics forum and stumbled onto query about primer, adapters that put me in thought about the process/pipeline I'm performing. I've Illumina paired-end 100bp,...
Forum: Bioinformatics 08-25-2017, 08:24 AM
Replies: 5
Views: 1,387
Posted By bio_informatics
I've not done Unifrac analyses but one issue...

I've not done Unifrac analyses but one issue while merging OTUs from different runs is that there can be duplicate OTUs.
That's why I suggested to merge FASTA from both runs, then cluster, remove...
Forum: Bioinformatics 08-24-2017, 04:05 AM
Replies: 5
Views: 1,387
Posted By bio_informatics
1- I'd take FASTA file before chimera checks from...

1- I'd take FASTA file before chimera checks from both the runs, merge, remove chimeras and proceed for classification.

2- Maybe reaching out to QIIME folks on their forum would be fruitful.
Forum: Bioinformatics 08-23-2017, 08:28 AM
Replies: 5
Views: 1,387
Posted By bio_informatics
I'd be hesitant in saying so. Different platforms...

I'd be hesitant in saying so. Different platforms employ different strategies to generate data. Even if you'd sent same samples in pyro and sanger machines it's possible to not have same thing...
Forum: Bioinformatics 06-20-2017, 01:43 PM
Replies: 3
Views: 1,075
Posted By bio_informatics
I have not worked in the direction you're...

I have not worked in the direction you're working. However, I've worked just fine with output from command line biom utility and/or R's biom package (from bioconductor).
Forum: Bioinformatics 06-20-2017, 11:19 AM
Replies: 3
Views: 1,075
Posted By bio_informatics
Are you using biom utility to perform the tasks...

Are you using biom utility to perform the tasks or scripts from QIIME?
Forum: Academic/Non-Profit Jobs 06-20-2017, 11:11 AM
Replies: 1
Views: 1,070
Posted By bio_informatics
Hi, Is the position still taking applications?

Hi,
Is the position still taking applications?
Forum: Academic/Non-Profit Jobs 06-20-2017, 11:06 AM
Replies: 1
Views: 843
Posted By bio_informatics
Is the position still open?

Is the position still open?
Forum: Bioinformatics 09-09-2016, 05:17 AM
Replies: 6
Views: 1,968
Posted By bio_informatics
Hi brian, Yes, I am looking for whatever...

Hi brian,
Yes, I am looking for whatever matches.
Forum: Bioinformatics 09-08-2016, 08:23 AM
Replies: 6
Views: 1,968
Posted By bio_informatics
Thank you for your reply. I am unable to below...

Thank you for your reply. I am unable to below work flow:


1- Would I get any quantitative evidence?



Yes, this is exactly what I'm doing. BLAST v3-v4 region against my sequences. :)
Forum: Bioinformatics 09-08-2016, 07:39 AM
Replies: 6
Views: 1,968
Posted By bio_informatics
Hi, Thanks for your reply. I'm trying to...

Hi,

Thanks for your reply.
I'm trying to confirm if the downloaded sequences I've contain V3-V4 region in them of 16S rRNA gene.
Create custom database to verify if my V3-V4 region is available...
Forum: Bioinformatics 09-07-2016, 07:10 AM
Replies: 6
Views: 1,968
Posted By bio_informatics
RDP: confirming V3-V4 region

Hi there,
I'm working on RDP training set for genera of our interests. For that I download sequences from link...
Forum: Bioinformatics 08-02-2016, 07:39 AM
Replies: 2
Views: 1,502
Posted By bio_informatics
Ah, I see. In the beginning from the options: ...

Ah, I see. In the beginning from the options:
Strain - type, non type, both

I selected both in radio button.

Thank you very much for your prompt reply, and helping me with this. :-)
Forum: Bioinformatics 08-02-2016, 06:56 AM
Replies: 2
Views: 1,502
Posted By bio_informatics
RDP: what does (T) mean in sequence identifier?

Hi There,
I'm downloading sequences from RDP (https://rdp.cme.msu.edu/hierarchy/hierarchy_browser.jsp?qvector=204&depth=0&openNode=0&currentRoot=0&searchStr=) for genera, and species I'm interested...
Forum: Bioinformatics 07-26-2016, 12:49 PM
Replies: 4
Views: 3,301
Posted By bio_informatics
Did you get any lead on this? I've similar query...

Did you get any lead on this? I've similar query at this (http://seqanswers.com/forums/showthread.php?t=70502) page.
Forum: Bioinformatics 07-26-2016, 07:12 AM
Replies: 0
Views: 1,606
Posted By bio_informatics
RDP classifier - training set: how do I create?

Hi there,

I've nasal and genital microbiome: 16S rRNA, Illumina 300BP, paired end data. For various reasons green-genes, and silva database don't solve our project's purpose, and thus we don't use...
Forum: Bioinformatics 07-26-2016, 06:21 AM
Replies: 8
Views: 4,418
Posted By bio_informatics
Late here: Last I recall installing, ea-utils...

Late here:
Last I recall installing, ea-utils needed libgsl-dev library to install
Forum: Bioinformatics 05-11-2016, 08:28 AM
Replies: 7
Views: 3,035
Posted By bio_informatics
Hi GM, I agree with what you said. I really...

Hi GM,
I agree with what you said. I really doubt data on my end, but I'm limited to my thoughts, and opinions.
This data lose of 33% is something sequencing center is unaware of, and weighing on...
Forum: Bioinformatics 05-11-2016, 08:03 AM
Replies: 7
Views: 3,035
Posted By bio_informatics
Hi GM, Yes, I get what you're saying. Wow,...

Hi GM,
Yes, I get what you're saying.
Wow, we both got what we both were saying seldom has that happened with me. ;)

Sequencing center sits in a different location, any direct criticism on...
Forum: Bioinformatics 05-11-2016, 07:46 AM
Replies: 7
Views: 3,035
Posted By bio_informatics
Hi GenoMax, Thank you for your reply. Yes, I...

Hi GenoMax,
Thank you for your reply.
Yes, I used this flag, posted relevant URL where I found solution, a reply ahead of you. :)

I'm working with 16S data, which uses complicated process, and...
Forum: Bioinformatics 05-11-2016, 07:35 AM
Replies: 7
Views: 3,035
Posted By bio_informatics
Found solution, finally. ...

Found solution, finally.

https://www.biostars.org/p/47203/

-task blastn-short

is crucial
Forum: Bioinformatics 05-11-2016, 07:12 AM
Replies: 7
Views: 3,035
Posted By bio_informatics
BLAST: no output

Hi,

BLAST 2.2.30+

I've 16 nucleotide base sequences, which I'd like to use to gather pairwise identity against another FASTA file.


makeblastdb -in barcode.fasta -dbtype nucl -out...
Forum: Bioinformatics 04-04-2016, 09:35 AM
Replies: 0
Views: 2,213
Posted By bio_informatics
Mapping assembled genome back to reads: why SNPs?

Hi members,

I've paired end, Illumina, Klebsiella Pneumonia.
Read length 251, MiSeq run
Quality remains good until the read end.

Assembled genome's quality is reasonable checked with Quast....
Forum: Bioinformatics 02-16-2016, 06:24 AM
Replies: 2
Views: 1,821
Posted By bio_informatics
Hi westerman, Thanks much for your reply. I...

Hi westerman,
Thanks much for your reply.
I see, it makes sense what Jeremy suggested, for the prevalent confusion of 'L' and 'N'.

I agree merely N, L 50s would be worthless if we overlook other...
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