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Forum: Bioinformatics 03-22-2017, 07:42 AM
Replies: 0
Views: 1,368
Posted By cbaudo
Visualize just non-synonymous variants in IGV

Hello,

I used snpeff to annotate a set of variants and I would like to only visualize where a particular type of variant (non-synonymous mutations) localize on the chromosomes in the IGV.

Is...
Forum: RNA Sequencing 02-23-2017, 07:52 AM
Replies: 3
Views: 2,687
Posted By cbaudo
vilperte, would you mind sharing your workflow...

vilperte, would you mind sharing your workflow for obtaining that geneset and using it with ade4? thank you
Forum: Bioinformatics 09-08-2016, 10:52 AM
Replies: 0
Views: 1,288
Posted By cbaudo
CummeRbund PCAplot RNA-sequencing

Hello all,

I'm using the PCAplot function in cummerbund and I was wondering if anyone knows how to display the variance explained for each principal component. The current code does not calculate...
Forum: Bioinformatics 03-17-2016, 09:22 AM
Replies: 2
Views: 1,079
Posted By cbaudo
Thanks Geno!

Thanks Geno!
Forum: Bioinformatics 03-17-2016, 08:59 AM
Replies: 2
Views: 1,079
Posted By cbaudo
Alignment to multiple reference sequences

Hello,

I'm interested in determining if plasmid sequences are in a NGS data set and I was thinking about creating a master fasta file with the sequences for each plasmid and then aligning NGS data...
Forum: Bioinformatics 02-24-2016, 12:18 PM
Replies: 0
Views: 2,969
Posted By cbaudo
Modify cummeRbund plots in R studio: color, error bar width

Hello everyone,

I would like to reduce the horizontal length of the whiskers on the error bars on my expression plots, modify the color on my bar plots to black, and remove the quant type beneath...
Forum: Bioinformatics 01-27-2016, 09:17 AM
Replies: 5
Views: 1,786
Posted By cbaudo
@GenoMax Could you suggest a PacBio aligner...

@GenoMax

Could you suggest a PacBio aligner that is capable of doing this as well?
Forum: Bioinformatics 01-27-2016, 08:47 AM
Replies: 5
Views: 1,786
Posted By cbaudo
Many thanks

Many thanks
Forum: Bioinformatics 01-27-2016, 08:25 AM
Replies: 5
Views: 1,786
Posted By cbaudo
BOWTIE2: How to randomly map a read to single alignment when read is multimapping?

I want to keep only one alignment per read, so if a read maps equally well to several locations, one location should be chosen at random. Could you help me identify the option to use in Bowtie2 to...
Forum: Bioinformatics 11-24-2015, 07:55 AM
Replies: 0
Views: 1,713
Posted By cbaudo
Cummerbund Standard Error, Gene Plot Visual Tweaking

Can I extract the expression level information and standard error for my samples from cummerbund in R studio? I'd like to be able to generate my own gene expression level plots for aesthetic reasons....
Forum: Bioinformatics 04-09-2015, 07:50 AM
Replies: 0
Views: 2,210
Posted By cbaudo
Reassign mapping quality in STAR / GATK/ Cufflinks compatibility

Hello all,

I'm reassigning mapping quality values produced by STAR from 255 to 60 (column 5 of the output) for GATK compatibility and I was wondering if this will have any effect on Cufflinks...
Forum: Bioinformatics 03-31-2015, 10:29 AM
Replies: 3
Views: 2,975
Posted By cbaudo
Cuffmerge error

Hello, I am getting the following error message when using Cuffmerge:

cas-mw134-9sb9s:cufflinks-2.2.1.OSX_x86_64 bioadmin$ ./cuffmerge p 30 -g genes_sort.gtf -s reference.txt assembly.txt

[Tue...
Forum: Bioinformatics 03-25-2015, 06:45 AM
Replies: 3
Views: 2,374
Posted By cbaudo
I've read conflicting information about marking...

I've read conflicting information about marking duplicates, do you suggest that I don't perform this step? Note that I haven't removed the duplicated reads.

Also, when you say it's becoming...
Forum: Bioinformatics 03-25-2015, 06:25 AM
Replies: 3
Views: 2,374
Posted By cbaudo
Can I use preproccesed bam files for Cufflinks?

This question has been asked here previously: http://seqanswers.com/forums/showthread.php?t=42408&highlight=cufflinks+preprocessed

Similarly, I have trimmed, aligned and sorted using STAR, add...
Forum: RNA Sequencing 03-04-2015, 04:59 AM
Replies: 3
Views: 3,514
Posted By cbaudo
Many thanks, Leon.

Many thanks, Leon.
Forum: RNA Sequencing 03-03-2015, 08:31 AM
Replies: 3
Views: 3,514
Posted By cbaudo
2nd Pass Alignment with STAR for RNA-sequencing

Hello everyone,

Firstly, thanks for reading this post. I'm performing 2nd pass alignment with STAR and I was wondering how to merge SJ.out.tab files. I'll be performing the first phase alignment...
Forum: Bioinformatics 02-19-2015, 12:01 PM
Replies: 5
Views: 3,677
Posted By cbaudo
kmcarr, What are the differences between...

kmcarr,

What are the differences between TruSeq3-PE.fa and TruSeq3-PE-2.fa? I've downloaded the latest release of Trimmomatic and have access to the PE-2 fasta file.

Thanks.
Forum: Bioinformatics 02-19-2015, 11:59 AM
Replies: 5
Views: 3,677
Posted By cbaudo
GenoMax and kmcarr, Thank you both for your...

GenoMax and kmcarr,

Thank you both for your responses. They have been extremely helpful.
Forum: Bioinformatics 02-18-2015, 07:51 AM
Replies: 5
Views: 3,677
Posted By cbaudo
Trimmomatic and Multiplexed Samples

Hello and thanks for reading,

I'm performing adapter trimming for the first time using Trimmomatic on paired-end reads. We solicited a third party to generate our RNA-seq libraries and they used...
Forum: RNA Sequencing 02-26-2014, 01:56 PM
Replies: 4
Views: 2,482
Posted By cbaudo
Thanks sindrle, I've successfully imported by...

Thanks sindrle,
I've successfully imported by data into R and labeled the points on the scatterplot with gene IDs, but I am encountering another issue. I would like to modify the axis intervals in...
Forum: RNA Sequencing 02-17-2014, 03:19 PM
Replies: 4
Views: 2,482
Posted By cbaudo
Hello orthodoc, I was wondering if you found...

Hello orthodoc,

I was wondering if you found a solution to this problem.

Thank you,
cbaudo
Showing results 1 to 21 of 21

 


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