Search found 22 matches

by jitendrakeshri
Mon Jan 15, 2018 3:08 am
Forum: Journal club
Topic: 16S database of medically important bacteria
Replies: 2
Views: 474

Re: 16S database of medically important bacteria

Thank you for clarification!
by jitendrakeshri
Sun Jan 14, 2018 10:12 am
Forum: Journal club
Topic: Classification up to species level
Replies: 2
Views: 284

Re: Classification up to species level

Thanks Pat for clearing my doubt!

Regards,
Jitendra
by jitendrakeshri
Tue Jan 09, 2018 8:22 am
Forum: Journal club
Topic: 16S database of medically important bacteria
Replies: 2
Views: 474

16S database of medically important bacteria

Hi,
I wish to see the curated 16S database for medically important bacteria.

In literature, there was one suggestion of 16SpathDB.

http://147.8.74.24/16SpathDB/main.php

Unforntunately, it is not working now. Can anyone suggest similar database?
by jitendrakeshri
Tue Jan 09, 2018 8:15 am
Forum: Journal club
Topic: Classification up to species level
Replies: 2
Views: 284

Classification up to species level

Hi, I wonder if we can classify the 16s rRNA data up to species level. I was going through the EzBioCloud 16S database and there was suggestions that we can classify 16S ngs data up to species level. They have curated formats are compatible with QIIME and MOTHUR pipelines. https://www.ezbiocloud.net...
by jitendrakeshri
Thu Apr 27, 2017 3:19 am
Forum: Commands in mothur
Topic: Unifrac and NMDS
Replies: 3
Views: 656

Re: Unifrac and NMDS

I have tried NMDS based on unifrac distances, but could not get the desired groupings. Please suggest.

The weighted unifrac analysis between lakes is as:

Tree# Groups WScore WSig
1 High FIC lakes - Low FIC lakes 0.679546 <0.0010

Regards,
by jitendrakeshri
Fri Apr 21, 2017 3:41 pm
Forum: Commands in mothur
Topic: Unifrac and NMDS
Replies: 3
Views: 656

Re: Unifrac and NMDS

Thanks Campenr for quick and informative reply. I will try NMDS based on Unifrac metric and see the difference.

Regards,
by jitendrakeshri
Thu Apr 20, 2017 7:16 am
Forum: Commands in mothur
Topic: Unifrac and NMDS
Replies: 3
Views: 656

Unifrac and NMDS

In core microbiome analysis, only 3 OTUs out of 1232 OTUs were shared among all samples at the relative abundance of 0.01. We have two groups of samples which are significantly different on the basis unifrac weighted analysis. But in NMDS plot based on thetayc distance does not show clustering of th...
by jitendrakeshri
Sun Feb 12, 2017 5:20 am
Forum: Commands in mothur
Topic: Aligned ITS reference files
Replies: 1
Views: 435

Aligned ITS reference files

Please suggest from where the ITS aligned reference fasta file can be downloaded?

I have tried from the link https://www.mothur.org/wiki/UNITE_ITS_database

but the mothur returns at pcr.seq command with "seqs are not aligned. When using start and end your sequences must be aligned."
by jitendrakeshri
Mon Jan 09, 2017 6:53 am
Forum: Commands in mothur
Topic: make.contigs
Replies: 2
Views: 554

Re: make.contigs

Dear Westcott,

Thanks a lot for your helpful reply.
by jitendrakeshri
Wed Dec 21, 2016 3:29 am
Forum: Commands in mothur
Topic: make.contigs
Replies: 2
Views: 554

make.contigs

Make.contigs failed as number of forward and reverse sequences are unequal. Please let me know the commands before making contigs at this stage. I got the warning in mothur as "Processing file pair 18J_S43_L001_R1_001.fastq - 18J_S43_L001_R2_001.fastq (files 1 of 1) <<<<< [ERROR]: You have 99010 seq...