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Forum: RNA Sequencing 04-28-2016, 05:00 AM
Replies: 7
Views: 2,170
Posted By illinu
Hi Devon, Thank you for replying. If I...

Hi Devon,

Thank you for replying. If I understand correct I should avoid the LRT test? I could use the interaction term like so:
resGenotype <- results(ddsM,...
Forum: RNA Sequencing 04-27-2016, 06:51 AM
Replies: 7
Views: 2,170
Posted By illinu
Thank you, I would like to know why the second...

Thank you, I would like to know why the second option is statistically incorrect.

And for sanity could you or someone confirm that this is the correct code in R (DESeq2 package):
...
Forum: RNA Sequencing 04-27-2016, 06:07 AM
Replies: 7
Views: 2,170
Posted By illinu
My biological question is how do genotype A and B...

My biological question is how do genotype A and B respond differently to the treatment. I need to take both factors into account. I wan't to know what's the difference between doing multifactor...
Forum: RNA Sequencing 04-27-2016, 04:50 AM
Replies: 7
Views: 2,170
Posted By illinu
multifactor analysis or pairwise comparison?

I can't find a simple answer to what's the difference between doing multifactor analysis or pairwise comparisons, example:

I have two factors to consider: condition (treatment or control) and...
Forum: Bioinformatics 02-03-2016, 12:02 AM
Replies: 4
Views: 2,197
Posted By illinu
Did you get this solved?

Did you get this solved?
Forum: Bioinformatics 06-04-2015, 10:43 PM
Replies: 6
Views: 2,392
Posted By illinu
You have a lot of options but for bacteria look...

You have a lot of options but for bacteria look at MIRA, Ray, Abyss, Velvet... I find that depending on the species one software might perform better than other so you have to try several and see...
Forum: Bioinformatics 06-03-2015, 05:13 AM
Replies: 252
Views: 104,319
Posted By illinu
I was running the...

I was running the SSPACE-STANDARD-3.0_linux-x86_64 in my computer and was getting that error, then I changed to the cloud and could chose another perl version (I was getting some perl errors, like...
Forum: Bioinformatics 04-14-2015, 12:57 AM
Replies: 252
Views: 104,319
Posted By illinu
Same as few posts above, I am trying the new...

Same as few posts above, I am trying the new SSPACE_Standard_v3.0_linux and get the same problem, first:


and when I do -x 0 I get this other error:


Is this due to the version, I got it...
Forum: Bioinformatics 03-12-2015, 06:05 AM
Replies: 4
Views: 1,252
Posted By illinu
Yes, when I sort by the subject hit I clearly see...

Yes, when I sort by the subject hit I clearly see when two or more isoforms are duplicated or not (when the subject start-end position overlaps between the two isoforms) or multiassembled (when each...
Forum: Bioinformatics 03-12-2015, 05:12 AM
Replies: 4
Views: 1,252
Posted By illinu
The blast report is a tab separated file, the...

The blast report is a tab separated file, the transcritps in fasta, but I am also producing a GTF3 file with another annotator
Forum: Bioinformatics 03-12-2015, 03:34 AM
Replies: 4
Views: 1,252
Posted By illinu
identify duplicated transcripts from blast report

I am working with a transcriptome assembled de novo. After a blastx analysis I kept the besthits (one hit per isoform) from which I isolated those annotations that are present more than once...
Forum: Bioinformatics 03-12-2015, 03:27 AM
Replies: 5
Views: 3,277
Posted By illinu
How did you get your count data matrix? I use the...

How did you get your count data matrix? I use the trinity pipeline for this analysis because it does all, align the reads to the transcriptome, calculate abundance, normalize and output the matrix...
Forum: Bioinformatics 02-23-2015, 06:24 AM
Replies: 0
Views: 1,152
Posted By illinu
Tool to find reads bridging two scaffolds?

I have a set of PacBio reads and I need to find which of them actually bridge two scaffolds of an existing assembly.

So far I've tried blasting the PacBio reads to the scaffolds of the assembly...
Forum: Bioinformatics 01-23-2015, 05:32 AM
Replies: 3
Views: 1,382
Posted By illinu
This is the document I needed, the Manual doesnt...

This is the document I needed, the Manual doesnt explain much on this. Thank you

Is there a way to extract only paired unaligned reads?
Forum: Bioinformatics 01-23-2015, 04:56 AM
Replies: 3
Views: 1,382
Posted By illinu
samtools F option

Hi,

Can someone explain here what the -F option in samtools means?
-F INT Skip alignments with bits present in INTwhat does it mean an alignment with for example 4 bits and why would you want...
Forum: Bioinformatics 11-21-2014, 07:38 AM
Replies: 12
Views: 5,247
Posted By illinu
Did you get the paths to nucmer with $ which...

Did you get the paths to nucmer with
$ which nucmer

I have it in /usr/bin/nucmer but you might have it elsewhere... check that well. Check it for all.

Also make sure you write ...
Forum: Bioinformatics 11-21-2014, 07:20 AM
Replies: 12
Views: 5,247
Posted By illinu
Yes, change ...

Yes, change
CISA=/home/user/Illumina/software/CISA1.3/CISA.py
for
CISA=/home/user/Illumina/software/CISA1.3
Forum: RNA Sequencing 11-13-2014, 01:25 AM
Replies: 0
Views: 1,823
Posted By illinu
Trinity output

Hi,
Trinity outputs to my understanding components and isoforms, or I think now they call them genes and transcripts, so can someone explain to me what are the different parts of the trinity output...
Forum: Bioinformatics 10-15-2014, 04:10 AM
Replies: 6
Views: 2,392
Posted By illinu
Let us know how it goes. I guess by hybrid it...

Let us know how it goes. I guess by hybrid it means short reads and PacBio??
I used a very close reference (2 My) to aid a de novo assembly with ALLPATHS-LG and I saw no improvement over the de novo...
Forum: Bioinformatics 10-14-2014, 12:28 AM
Replies: 3
Views: 1,797
Posted By illinu
fastx toolkit ...

fastx toolkit
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastq_to_fasta_usage
Forum: Bioinformatics 10-14-2014, 12:26 AM
Replies: 6
Views: 2,392
Posted By illinu
You can still use ALLPATHS-LG with the reference...

You can still use ALLPATHS-LG with the reference based assembly option
Forum: RNA Sequencing 09-25-2014, 07:19 AM
Replies: 6
Views: 1,631
Posted By illinu
It is eukariote diploid heterozygote... there...

It is eukariote diploid heterozygote... there could be alternative splicing due to the treatment (?)... not sure about pooling
Forum: RNA Sequencing 09-25-2014, 06:51 AM
Replies: 6
Views: 1,631
Posted By illinu
Good point... I don't know. Actually I am looking...

Good point... I don't know. Actually I am looking at how other people do DE with independently assembled transcriptomes, no reference genome and different genotypes and the options are so wide that I...
Forum: RNA Sequencing 09-25-2014, 12:09 AM
Replies: 6
Views: 1,631
Posted By illinu
This is exactly what I thought, too strict. So I...

This is exactly what I thought, too strict. So I did blastn finally.

I didn't think about pooling all samples because the 8 control + 8 treatment are not all the same genotype but 4 different...
Forum: RNA Sequencing 09-24-2014, 04:45 AM
Replies: 6
Views: 1,631
Posted By illinu
Preparing reference transcriptome: to or not to megablast

A quick question here. I am constructing a reference transcriptome for DE out of 16 transcriptomes (8 control + 8 treatment) and my strategy is as follows:
1. create a database with transcriptome...
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