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Search: Posts Made By: Kennels
Forum: Bioinformatics 11-17-2013, 11:17 PM
Replies: 9
Views: 3,926
Posted By Kennels
Just letting you know the script did what I...

Just letting you know the script did what I wanted.
I just modified the script a little:


#!/usr/bin/perl

use strict;
use warnings;
use Getopt::Long;
use Bio::SearchIO;
Forum: Bioinformatics 11-16-2013, 02:44 AM
Replies: 9
Views: 3,926
Posted By Kennels
Thanks I'll give it a try.

Thanks I'll give it a try.
Forum: Bioinformatics 11-15-2013, 02:56 AM
Replies: 9
Views: 3,926
Posted By Kennels
Yes and no. Also looking for partial...

Yes and no.
Also looking for partial alignment, but only those with single hsp.
Forum: Bioinformatics 11-15-2013, 01:52 AM
Replies: 9
Views: 3,926
Posted By Kennels
Thanks bambam, but that's not what I'm after. ...

Thanks bambam, but that's not what I'm after.

Yes that will pull out those with 1 match, but what I'm after is those that have only have one alignment 'section' (i.e. high-scoring segment pair). ...
Forum: Bioinformatics 11-14-2013, 07:39 PM
Replies: 9
Views: 3,926
Posted By Kennels
how to identify blast hits with only 1 HSP (not limit the number of HSP)

Hi,

Is there a way to identify blast hits where there was only one HSP to the database?

i.e. I don't want to limit the number of HSP's displayed, but I want to identify all queries which only...
Forum: Bioinformatics 10-28-2013, 06:33 PM
Replies: 11
Views: 2,350
Posted By Kennels
Thanks gringer for your explanation - it is...

Thanks gringer for your explanation - it is clearer now, and looking at the correlation output it makes more sense.

You were right that the log values seem to show overall a linear relationship...
Forum: Bioinformatics 10-28-2013, 05:17 PM
Replies: 2
Views: 1,881
Posted By Kennels
yes, it cannot find your R installation. Did you...

yes, it cannot find your R installation. Did you install it?
If so, try putting it in your PATH.
e.g.


export PATH=/path/to/R:$PATH


where /path/to/R is where you installed R.
Forum: Bioinformatics 10-28-2013, 05:09 PM
Replies: 11
Views: 2,350
Posted By Kennels
Thanks everyone for the advice and information. I...

Thanks everyone for the advice and information. I am currently testing out scatterplots and several correlation tests via R.

However... and I do apologize if this doesn't seem to be getting...
Forum: Bioinformatics 10-28-2013, 03:11 AM
Replies: 11
Views: 2,350
Posted By Kennels
Thanks for the reply, I suppose I can do all...

Thanks for the reply, I suppose I can do all pairwise comparisons for all samples and find the best correlation. But this would be assuming some kind of a linear relationship (?), and there is high...
Forum: Bioinformatics 10-27-2013, 07:38 PM
Replies: 2
Views: 1,135
Posted By Kennels
The software Trimmomatic can generate the orphans...

The software Trimmomatic can generate the orphans for you in addition to QC filter and removing adapters, all in one go. If you want interleaved PE reads, then just take the Paired files output and...
Forum: Bioinformatics 10-27-2013, 06:51 PM
Replies: 11
Views: 2,350
Posted By Kennels
Is Principal Component Analysis suited for this analysis?

Hi,

I have expression values (calculated by RSEM, RNAseq data) for over 30 genes, from 5 samples. Based on these values, I would like to find which two samples display the most 'similar'...
Forum: Bioinformatics 10-23-2013, 08:06 PM
Replies: 9
Views: 1,977
Posted By Kennels
your file size is zero - between 'students' and...

your file size is zero - between 'students' and 'Oct' .

You need to check where and how your downloaded your file. It should not be empty. Perhaps you can get it again from your source. Redo the...
Forum: Bioinformatics 10-23-2013, 07:59 PM
Replies: 9
Views: 1,977
Posted By Kennels
Well there's your problem - your fastq file is...

Well there's your problem - your fastq file is empty.
The head command gets the first 10 lines from your file.

what do you get with:

ls -lh NA11881.fastq
Forum: Bioinformatics 10-23-2013, 07:01 PM
Replies: 9
Views: 1,977
Posted By Kennels
Try also putting '-q' option to specify it is...

Try also putting '-q' option to specify it is fastq input.
If that still fails, what is the output from


head NA11881.fastq


some check questions:

Can you post any errors or warning you...
Forum: Bioinformatics 10-23-2013, 06:43 PM
Replies: 9
Views: 1,977
Posted By Kennels
Try specifying '-U' in front of your fastq file

Try specifying '-U' in front of your fastq file
Forum: Bioinformatics 10-22-2013, 10:51 PM
Replies: 10
Views: 5,055
Posted By Kennels
Thanks bambam for your input and advice. And...

Thanks bambam for your input and advice.
And you actually helped phrase my question better.

Yes I am more interested in identifying the SNV sites rather than assigning a genotype, but I was...
Forum: Bioinformatics 10-21-2013, 04:13 PM
Replies: 10
Views: 5,055
Posted By Kennels
Yes it is Nicotiana benthamiana :)

Yes it is Nicotiana benthamiana :)
Forum: Bioinformatics 10-21-2013, 04:06 PM
Replies: 10
Views: 5,055
Posted By Kennels
Thanks bambam for the information. The plant...

Thanks bambam for the information.

The plant I'm working on is a Nicotiana species (close relative to N. tabacco), and it's an allotetraploid, genome size between 2-3Gb, and probably 19 xsomes. ...
Forum: Bioinformatics 10-20-2013, 07:47 PM
Replies: 10
Views: 5,055
Posted By Kennels
diploid SNP caller on polyploid plant

Hi,

How would one interpret SNP calling results when applying reads from a polyploid plant, using diploid caller like samtools or default diploid option of GATK?
I'm able to get SNP calls, but...
Forum: Bioinformatics 10-09-2013, 04:25 PM
Replies: 3
Views: 1,533
Posted By Kennels
How close is your target species to D.mel ? Could...

How close is your target species to D.mel ? Could you alternatively align your reads to this with relaxed parameters, and use those that aligned to do a de novo assembly?

It also could be the...
Forum: Bioinformatics 10-09-2013, 03:47 PM
Replies: 3
Views: 1,533
Posted By Kennels
you might have assembled chimeric transcripts by...

you might have assembled chimeric transcripts by using all the reads from different sources. Kind of like a metagenomic assembly, so you might want to read some papers that contain information on...
Forum: Bioinformatics 10-02-2013, 05:58 PM
Replies: 2
Views: 1,793
Posted By Kennels
Hi, For example, it means you count the...

Hi,

For example, it means you count the number of small RNA that mapped to pos 0-250, then 25-275, then 50-300 and so on, and you plot the total number of mapped smallRNA in these 250nt bins.
Forum: Bioinformatics 10-01-2013, 11:16 PM
Replies: 15
Views: 7,152
Posted By Kennels
Hi I am doing a similar analysis to you, and...

Hi
I am doing a similar analysis to you, and have run BWA-MEM aligned files, and GATK v2.2-3.

Are you sure that GATK Unified Genotyper tool doesn't run when duplicates are not marked? I could...
Forum: Bioinformatics 09-30-2013, 12:35 AM
Replies: 1
Views: 2,266
Posted By Kennels
It is the alignment coordinates of the...

It is the alignment coordinates of the subsequence, representative sequence, strand, and identity.

For example, your representative sequence from this cluster would be sequence 3, denoted by the...
Forum: Bioinformatics 09-29-2013, 08:35 PM
Replies: 1
Views: 3,097
Posted By Kennels
I've run minimus2 before without setting any -D...

I've run minimus2 before without setting any -D parameters. The default for overlap is supposed to be 40, but in my log file it says the same as you: minimum overlap is 5.

So maybe this is just a...
Showing results 1 to 25 of 149

 


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