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Search: Posts Made By: nbahlis
Forum: Bioinformatics 05-11-2015, 08:54 PM
Replies: 1
Views: 855
Posted By nbahlis
DESeq2 and genomic ranges

Is it possible to create a bed file or extract the genomic coordinates (start, end and strand) from the list of DE genes generated by DESeq2?
Forum: RNA Sequencing 05-10-2015, 08:29 AM
Replies: 192
Views: 55,321
Posted By nbahlis
Is there a way to get the genomic coordinates...

Is there a way to get the genomic coordinates (including strand) in DESeq2 from the list of DE genes? I used HTseq to start with.
Forum: Bioinformatics 05-24-2014, 02:06 PM
Replies: 6
Views: 6,420
Posted By nbahlis
I have the same problem. Is there a way to rum...

I have the same problem. Is there a way to rum Mutect without removing duplicates (or presumed duplicates)?
Forum: Ion Torrent 04-15-2014, 05:56 AM
Replies: 14
Views: 5,360
Posted By nbahlis
That is typical with the proton. We are told by...

That is typical with the proton. We are told by lifetech that a22-24 score on the proton equals the 30 on the illumina platform. It has to do apparently withe the proton more conservative score...
Forum: RNA Sequencing 04-08-2014, 07:26 AM
Replies: 192
Views: 55,321
Posted By nbahlis
thanks Ryan. For whatever reason "select <-...

thanks Ryan. For whatever reason "select <- which(p.adjust( res$pvalue[keep], method="BH" ) < .1 )" does not select in the heatmap for the genes with padj<0.1. The list of the genes seems to be...
Forum: RNA Sequencing 04-08-2014, 06:28 AM
Replies: 192
Views: 55,321
Posted By nbahlis
here is the script I've written: > sampleFiles...

here is the script I've written:
> sampleFiles <- list.files(path="~/Desktop/HTseq_counts/", pattern="*.counts")
> Table3 <- data.frame(
+ sampleName = sampleFiles, fileName = sampleFiles,
+...
Forum: RNA Sequencing 04-08-2014, 06:20 AM
Replies: 192
Views: 55,321
Posted By nbahlis
Hi Ryan, What is the right way to draw the...

Hi Ryan,

What is the right way to draw the heat map based on genes with padj < 0.1 instead of selecting "Rowmeans" as in the vignette? The script I have written does NOT select genes based on...
Forum: RNA Sequencing 04-07-2014, 11:53 PM
Replies: 192
Views: 55,321
Posted By nbahlis
Hi Ryan. The script I used does not seem to...

Hi Ryan. The script I used does not seem to filter the genes based on padj < 0.1. I have followed the DESeq2 vignette and the only change I am introducing is the selection step for the genes based on...
Forum: RNA Sequencing 04-05-2014, 07:06 AM
Replies: 192
Views: 55,321
Posted By nbahlis
thank you Ryan, do you mean I need to transform...

thank you Ryan, do you mean I need to transform my data with rld before I select a subset?
Forum: RNA Sequencing 04-04-2014, 09:34 PM
Replies: 192
Views: 55,321
Posted By nbahlis
DEseq and Heatmap

Can someone please advise what is the best script to create a heatmap with only differentially expressed genes? I've tried the script below and I am not sure this is correct way to do it

> select...
Forum: Bioinformatics 12-01-2013, 08:17 AM
Replies: 27
Views: 5,604
Posted By nbahlis
Many thanks!

Many thanks!
Forum: Bioinformatics 11-30-2013, 01:10 PM
Replies: 27
Views: 5,604
Posted By nbahlis
Hi Alejandro Is there a way to figure out...

Hi Alejandro

Is there a way to figure out what the bin number exactly represents. In other words what exon or exon-fusion/splice it represents?

thank you
Forum: Bioinformatics 11-20-2013, 07:20 AM
Replies: 22
Views: 10,086
Posted By nbahlis
thank you, I will give this a try and see if the...

thank you, I will give this a try and see if the results differ significantly
Forum: Bioinformatics 11-20-2013, 07:13 AM
Replies: 22
Views: 10,086
Posted By nbahlis
thank you for the quick reply. I am attempting to...

thank you for the quick reply. I am attempting to identify genes involved in resistance to treatment "X". RNAseq were done on samples collected from individual patients pre-treatment and at the time...
Forum: Bioinformatics 11-20-2013, 06:46 AM
Replies: 22
Views: 10,086
Posted By nbahlis
Hi Ryan, DESeq2 question Is the script...

Hi Ryan,

DESeq2 question
Is the script below the correct way to set up a comparison between paired samples pre- and post treatment?
thank you
> sampleFiles <-...
Forum: Bioinformatics 11-16-2013, 06:27 AM
Replies: 27
Views: 5,604
Posted By nbahlis
thank you Alejandro they are paired data...

thank you Alejandro

they are paired data /samples. Can you please advise how to add the pairing as a variable. I will repeat the analysis with better (strict) filtering of the counts.
Thank you...
Forum: Bioinformatics 11-15-2013, 07:31 PM
Replies: 11
Views: 4,981
Posted By nbahlis
DEXSeq exon bins

Thank you for this useful discussion.
If I understand correctly the "exon bins" to not correspond to actual exons?
I did run DEXSeq on 22 samples with condition pre- and post-treament. Inspecting...
Forum: Bioinformatics 11-14-2013, 08:31 PM
Replies: 27
Views: 5,604
Posted By nbahlis
Hello Alejandro and Ryan I ran DEXSeq on 22...

Hello Alejandro and Ryan

I ran DEXSeq on 22 samples (2 conditions: pre and post, biological replicates) as per my post earlier. I did get 50 warnings after running > ecs <- estimateDispersions (...
Forum: Bioinformatics 11-12-2013, 02:32 AM
Replies: 27
Views: 5,604
Posted By nbahlis
it worked now! I just didn't have to specify...

it worked now! I just didn't have to specify "stringsAsFactor". Without it worked fine. Thank you Alejandro and Ryan for your great work
Forum: Bioinformatics 11-12-2013, 02:21 AM
Replies: 27
Views: 5,604
Posted By nbahlis
error with DEXeq

Hi Alejandro and dpryan,

I did use as.character and I am getting the following error"
Error: all(unlist(lapply(design, class)) == "factor") is not TRUE

Any help or advice is greatly...
Forum: RNA Sequencing 06-22-2013, 11:26 AM
Replies: 5
Views: 2,772
Posted By nbahlis
KeyError: 'score'

same error here, anyone figured out the problem? It was running fine a week ago? so nothing to do with the way I compiled these files.
Forum: Bioinformatics 06-17-2013, 11:21 AM
Replies: 40
Views: 18,900
Posted By nbahlis
I was getting an empty tophat-fusion-post...

I was getting an empty tophat-fusion-post results. I am working with Ion Proton reads, ie single stranded reads. The problem was in the command for the top hat-fusion-post
"tophat-fusion-post -p 8...
Forum: Bioinformatics 06-07-2013, 03:06 PM
Replies: 5
Views: 2,626
Posted By nbahlis
thanks Jonathan, just started the analysis with...

thanks Jonathan, just started the analysis with Seurat, looks its gonna take FEW hours. I tweaked the script to add more memory to Java " java -Xmx2g -jar Seurat.jar ...". Without adding "-Xmx2g" I...
Forum: Bioinformatics 06-06-2013, 05:09 AM
Replies: 5
Views: 2,626
Posted By nbahlis
is is possible to run Seurat without RNAseq data?

is is possible to run Seurat without RNAseq data?
Forum: Bioinformatics 05-27-2013, 07:15 AM
Replies: 5
Views: 9,386
Posted By nbahlis
Tophat and Proton

Did anyone figure out the type of library to use with Ion Torrrent Proton reads when using tophat? --library-type specified as either fr-firststrand or fr-secondstrand?
Also has anyone used...
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