SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 94
Search took 0.05 seconds.
Search: Posts Made By: Zapages
Forum: Bioinformatics 11-25-2016, 08:24 PM
Replies: 10
Views: 2,422
Posted By Zapages
Very interesting development and something that I...

Very interesting development and something that I always thought about this too when I was working on my data sets.




Thank you for sharing.

I did a lot of RNA-Seq analysis last year and...
Forum: Bioinformatics 11-25-2016, 02:31 PM
Replies: 10
Views: 2,422
Posted By Zapages
I would trim up the first 19 bps at the 5' end...

I would trim up the first 19 bps at the 5' end (which probably are the adapters) and trim the last 50 bps at the 3' end.

Also I would suggest increasing the kmer count to k 10 in FastQC to get a...
Forum: Bioinformatics 11-25-2016, 07:10 AM
Replies: 3
Views: 2,432
Posted By Zapages
I would leave the unpaired files alone. It...

I would leave the unpaired files alone.

It all depends on what type of analysis are you trying to conduct?

If you are working on De-novo or novel assembled genomes.

Then the foremost step...
Forum: Bioinformatics 11-24-2016, 10:57 PM
Replies: 3
Views: 2,432
Posted By Zapages
All you need is Forward_Paired and Reverse_Paired...

All you need is Forward_Paired and Reverse_Paired reads. Those reads can be merged together using FLASH, a custom script (there are few here or on Biostar), or you may use Cyverse's Discovery...
Forum: Bioinformatics 11-24-2016, 02:48 PM
Replies: 6
Views: 1,519
Posted By Zapages
Merging the reads into one file depends on the...

Merging the reads into one file depends on the task that you are working on.

and also do some quality control on the sequences.

Please FastQC to check the quality of after each trimming...
Forum: Bioinformatics 04-30-2016, 11:41 AM
Replies: 2
Views: 694
Posted By Zapages
^As mentioned above. They are overlapping genes,...

^As mentioned above. They are overlapping genes, I would suggest taking a look at them through NCBI IGV to get a better idea on how things are.

Also check to see that it might be Isoforms if you...
Forum: Bioinformatics 04-30-2016, 11:36 AM
Replies: 0
Views: 909
Posted By Zapages
Heatmap with replicate/triplicate data sets in R

Hi Everyone,

I have Control and Treated data sets that I have gone through HTSeq-counts and did differential expression gene analysis through EdgeR, DESeq, and DESeq2.

My pipeline is:
...
Forum: Bioinformatics 02-03-2016, 01:19 PM
Replies: 8
Views: 1,989
Posted By Zapages
Hi I just tested the program out again with...

Hi

I just tested the program out again with all of my RNA-Seq datasets. It works really great. Thank you for creating this application.

Maybe to help users create publication like...
Forum: RNA Sequencing 02-03-2016, 08:46 AM
Replies: 2
Views: 714
Posted By Zapages
That is interesting, but should we take this FPKM...

That is interesting, but should we take this FPKM value for this number as something to be highly expressed or should we take a look at isoforms and see the confidence intervals to consider its true...
Forum: RNA Sequencing 02-02-2016, 06:09 PM
Replies: 2
Views: 714
Posted By Zapages
Cuffdiff Question with FPKM of one sample being 0

Hi Everyone,

I have question in regards to cuffdiff. I have the following data in tissue 1 vs tissue 2.



Sample A: 0 Sample B: 20.292 Log2 Change(fold change): 1.79769e+308


My...
Forum: RNA Sequencing 01-30-2016, 04:19 PM
Replies: 0
Views: 875
Posted By Zapages
Generating Intron GTF or GFF3 file for RNA-Seq Analysis

Hi Everyone,

I am trying to create a custom GTF or GFF3 file that I hope to use to do RNA-Seq analysis. The reason to do this analysis is to check on conserved introns that we are finding in our...
Forum: Bioinformatics 01-25-2016, 12:33 PM
Replies: 8
Views: 1,989
Posted By Zapages
Yes, I agree this work definitely is useful and...

Yes, I agree this work definitely is useful and has a place. As this could be specifically designed for cuffdiff and other R based tool sets.

Currently, using gplot2 to create heatmaps takes a...
Forum: Bioinformatics 01-25-2016, 08:20 AM
Replies: 8
Views: 1,989
Posted By Zapages
Hi I was just testing the program out. ...

Hi

I was just testing the program out. This seems to be a great way to help non-Bioinformaticians to visualize their differential expression data.

There is an extra ")" at the end of the...
Forum: Bioinformatics 06-29-2015, 10:31 PM
Replies: 5
Views: 1,257
Posted By Zapages
Hi Genomax, Thank you Genomax. I'm...

Hi Genomax,

Thank you Genomax. I'm definitely using gene prediction programs as well. I'm trying to build confidence on newly denovo/ NCBI assembled sequences for a specific group of gemes of...
Forum: Bioinformatics 06-29-2015, 03:06 PM
Replies: 5
Views: 1,257
Posted By Zapages
Obtaining ORFs from DNA sequence

Hi Everyone,

I have small question in regards to obtaining ORFs in DNA sequences. I know that EMBOSS tools have a collection of awesome tools to do this specifically.

I have used six-pack from...
Forum: Bioinformatics 06-20-2015, 01:13 PM
Replies: 14
Views: 5,729
Posted By Zapages
You might want to try Vennt to create Venn...

You might want to try Vennt to create Venn Diagrams: http://drpowell.github.io/vennt/

PS: I have used Vent before and it works fairly well from my own experience. :)
Forum: Bioinformatics 06-14-2015, 11:41 AM
Replies: 3
Views: 1,066
Posted By Zapages
I would suggest using MIRA in Geneious as well....

I would suggest using MIRA in Geneious as well. Its really good with Viral genomes.

All the best with your project. :)
Forum: Bioinformatics 05-14-2015, 08:24 AM
Replies: 4
Views: 2,475
Posted By Zapages
I would adjust adjusting the False Discovery Rate...

I would adjust adjusting the False Discovery Rate a bit, but more importantly increase the maximum number of fragments allows more gene Ids to be found. I believe the default is 1 Million.

I had...
Forum: Bioinformatics 05-13-2015, 01:57 PM
Replies: 212
Views: 56,875
Posted By Zapages
Hi Brian, Thank you for creating these...

Hi Brian,

Thank you for creating these awesome applications. I was wondering if you have any plans to create an OLC aligner or something that improves Dedupe so that it can merge multiple...
Forum: Bioinformatics 05-12-2015, 04:49 PM
Replies: 1
Views: 815
Posted By Zapages
Newbler Illumina Paired End Reads - Interleave or not to interleave?

Hi Everyone,

Thew Newbler documentation has been very bare bone from what I have been able to gather. I have been able to successfully install Newbler with GUI on our Ubuntu (Bio Linux 8)...
Forum: Bioinformatics 05-12-2015, 09:03 AM
Replies: 3
Views: 1,077
Posted By Zapages
Thank you Phillip and Genomax. Both of the...

Thank you Phillip and Genomax. Both of the strategies work. :)

Really appreciate all the help.

Many Thanks,

Zapages
Forum: Bioinformatics 05-09-2015, 02:18 PM
Replies: 3
Views: 1,077
Posted By Zapages
Adding counting Contig number at the start of Fasta Header

I am trying to add Prefix to a list of Fasta sequences (30K+ which I have de-novo assembled) in a fasta file at the same time.

I know from the past that have been able to add it at the end of the...
Forum: Bioinformatics 05-08-2015, 03:55 AM
Replies: 278
Views: 97,430
Posted By Zapages
I am trying to assemble 275 paired end Illumina...

I am trying to assemble 275 paired end Illumina reads that I have interleaved together. Previously I was successfuly ran the interleaved files at the Kmer value 137. I compiled latest Ray version...
Forum: Bioinformatics 03-02-2015, 10:23 AM
Replies: 5
Views: 2,620
Posted By Zapages
Please check my answer out on Iplant regards to...

Please check my answer out on Iplant regards to importing Cuffdiff2 data:...
Forum: Illumina/Solexa 02-23-2015, 06:11 AM
Replies: 7
Views: 1,118
Posted By Zapages
My suggestion is to try slew of different...

My suggestion is to try slew of different assemblers and different k-mer values.

In terms of genome assembly, the larger the k-mer the better the assembly as you are reducing redundancy in the...
Showing results 1 to 25 of 94

 


All times are GMT -8. The time now is 02:32 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO