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Forum: General 06-29-2018, 11:04 AM
Replies: 0
Views: 1,062
Posted By arcolombo698
ArrayControl RNA Spike Ins

Hello. I am looking for the transcripts for ArrayControl RNA spike ins and was wondering if anyone could share the transcript spike ins. I am re-analyzing another lab's experiment who used the...
Forum: Introductions 06-04-2015, 10:40 AM
Replies: 11
Views: 2,216
Posted By arcolombo698
FastQC does plot this information so one can...

FastQC does plot this information so one can visually see the distribution of length. this is a quick/easy approach.

if you use samtools, one can plot the lengths using R.
Forum: Bioinformatics 03-24-2015, 07:08 PM
Replies: 1
Views: 1,146
Posted By arcolombo698
Conceptual Poor Alignment Understanding

Hello.
I am working on some RNAseq and received a few poor reads from our sample set. One possible undersatnding is cDNA contamination. note we aligned untrimmed reads because if there is "junk" in...
Forum: Bioinformatics 07-28-2014, 08:46 AM
Replies: 6
Views: 1,637
Posted By arcolombo698
Yes thank you... it is true that CNV analysis...

Yes thank you... it is true that CNV analysis must have WGS or WES. thank you very much.
Forum: Bioinformatics 07-25-2014, 03:48 PM
Replies: 6
Views: 1,637
Posted By arcolombo698
can CNVer be used on RNAseq (NGS short mated...

can CNVer be used on RNAseq (NGS short mated reads) ?
Forum: Bioinformatics 07-25-2014, 02:27 PM
Replies: 2
Views: 883
Posted By arcolombo698
hi. First, it is hard to see from your post...

hi.

First, it is hard to see from your post but here is some sample data.

head(complete_cases)
chromosome start end test ref position log2 p.value cnv
7037 chr7...
Forum: Literature Watch 07-23-2014, 05:43 PM
Replies: 46
Views: 32,465
Posted By arcolombo698
Understanding the Log2 Ratio plotted

Hi. thank you in advance.
so after re-reading the manual, I have a question about the values for the y-axis.

The y-axis has the log2 data from the output in the .cnv file.

In the paper, it...
Forum: Bioinformatics 07-23-2014, 05:39 PM
Replies: 6
Views: 1,307
Posted By arcolombo698
do you know what the cnv column means? For...

do you know what the cnv column means?
For instance, say in R you use

data <- read.delim("test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.cnv")

this data$cnv is all integers.... do you know...
Forum: Bioinformatics 07-23-2014, 01:06 PM
Replies: 6
Views: 1,307
Posted By arcolombo698
regarding your original question about insertion...

regarding your original question about insertion and deletion. Im re-reading the paper. from page 2/9 the predicted copy number ratio is r = z * (N_Y)/(N_X). if this value is then log transformed,...
Forum: Literature Watch 07-21-2014, 04:59 PM
Replies: 46
Views: 32,465
Posted By arcolombo698
thank you for the response. What does the CNV...

thank you for the response. What does the CNV argument mean? and what does the glim argument mean? is the glim the limits on the p.value column in the data frame for data?

From the manual... ...
Forum: Literature Watch 07-21-2014, 04:06 PM
Replies: 46
Views: 32,465
Posted By arcolombo698
I am not a CGH expert by any means whatsoever. ...

I am not a CGH expert by any means whatsoever. From my experiments, the germline samples are the controls, which are tumor free. The tumor samples have tumors, and we are measuring the variation...
Forum: Literature Watch 07-16-2014, 06:51 PM
Replies: 46
Views: 32,465
Posted By arcolombo698
Rotating the X tick marks with plot.cnv

Thank you... I have a last question

when plotting, how do I rotate 90 degrees the x labels for each tick mark. I know with ggplot there is an angle option that can be used. right now my images...
Forum: Bioinformatics 07-16-2014, 06:45 PM
Replies: 6
Views: 1,307
Posted By arcolombo698
I am also interested in this. Do you know how to...

I am also interested in this. Do you know how to plot for a single chromosome? I am getting this error

plot.cnv(data,chromosome=12)
Error in if (glim[1] == 0) glim[1] <-...
Forum: Literature Watch 07-16-2014, 04:08 PM
Replies: 46
Views: 32,465
Posted By arcolombo698
@ Clarissa normally with CGH experiments you...

@ Clarissa

normally with CGH experiments you are comparing a tumor sample with a non-tumor sample. my data has a germline sample and also a tumor sample. the germline is used as a reference. So...
Forum: Literature Watch 07-16-2014, 04:02 PM
Replies: 46
Views: 32,465
Posted By arcolombo698
The manual does not specify that mouse genome is...

The manual does not specify that mouse genome is not allowed, has anyone used CNV-seq for mouse data?

I was able to add the genome.fa used under alignment under --genome parameter, but wish to...
Forum: Bioinformatics 07-16-2014, 04:00 PM
Replies: 2
Views: 739
Posted By arcolombo698
What I did was under --genome command, I...

What I did was under --genome command, I included the same fasta file used for alignment of the mouse genome.

However, I am not sure this is allowed. I know for RDxplorer, the manual says that...
Forum: Bioinformatics 07-16-2014, 03:23 PM
Replies: 3
Views: 2,063
Posted By arcolombo698
I stand corrected. thank you. RNAseq uses...

I stand corrected. thank you.

RNAseq uses cDNA, not quite the same as DNA from Whole Genome.

Basically there are two types of data used for CNV analysis WGS (whole genome DNA sequencing) and...
Forum: Bioinformatics 07-16-2014, 12:24 PM
Replies: 1
Views: 719
Posted By arcolombo698
according to ...

according to

https://github.com/Bioconductor/copy-number-analysis/wiki/CNV-seq

the BAM files can be processed using samtools command as a substitute for the best hits.pl scripts. yes.
...
Forum: Bioinformatics 07-16-2014, 11:40 AM
Replies: 1
Views: 719
Posted By arcolombo698
CNV-seq Manual Question

Hi. thank you in advance.

So I am reading through the manual of CNV-seq and have a question with this part:
question: I did not use BLAT or SOLID alignment tools, but used Tophat2 and have the...
Forum: Complete Genomics 07-16-2014, 11:36 AM
Replies: 1
Views: 3,397
Posted By arcolombo698
The only thing I have learned is that CNV-seq is...

The only thing I have learned is that CNV-seq is only useful if you used Solid alignment tools, or BLAT alignment tools, and CNV-seq is not useful for mouse data, but only human and chicken.
Forum: Bioinformatics 07-16-2014, 11:35 AM
Replies: 2
Views: 739
Posted By arcolombo698
Cnv-seq On Mouse Data

Hi, I am interested in using CNV-seq on mm10, however, when I use the command line the genome for mouse is not avail... is this CNV-seq software not useful for mm10 ref genomes?


...
Forum: Bioinformatics 07-16-2014, 11:18 AM
Replies: 3
Views: 2,063
Posted By arcolombo698
the manual says both. read their paper it is on...

the manual says both. read their paper it is on page 1
Forum: Bioinformatics 07-14-2014, 01:43 PM
Replies: 2
Views: 2,096
Posted By arcolombo698
I am working on this same issue, did you have any...

I am working on this same issue, did you have any progress here?
Forum: Bioinformatics 07-14-2014, 01:41 PM
Replies: 1
Views: 950
Posted By arcolombo698
I am also interested in this type of problem, did...

I am also interested in this type of problem, did you find a software or method to detect this information about copy number changes?
Forum: Bioinformatics 07-14-2014, 01:38 PM
Replies: 2
Views: 1,027
Posted By arcolombo698
I am also working on finding the copy number of a...

I am also working on finding the copy number of a gene in a genome... there is a post here that suggests using cufflinks to extract the FPKM scores, and aligning to the ORFs ... did you find a...
Showing results 1 to 25 of 142

 


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