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Forum: RNA Sequencing 04-23-2018, 01:39 PM
Replies: 0
Views: 1,184
Posted By Starr_Hazard
DEXseq in a docker environment

I am attempting to run a DEXseq python script to count reads from a STAR alignment to the human genome. I am trying to a “docker” procedure to setup the environment and execute the program.
...
Forum: Bioinformatics 11-19-2014, 01:20 PM
Replies: 3
Views: 1,139
Posted By Starr_Hazard
Good point about the subject line ...

Good point about the subject line
Mm_UCSC_Mm10_genome.gtf was used for TopHat/Bowtie2 to make the bam and by htseq-count to count

I believe default TopHat/Bowtie2 bams are coordinate/position...
Forum: Bioinformatics 11-19-2014, 10:33 AM
Replies: 3
Views: 1,139
Posted By Starr_Hazard
DESEq2 seems to under report counts for SE reads

Here are the Align summary data from TopHat for single-end reads. These SE Reads are NOT stranded.

cat /PATH/align_summary.txt | grep Mapped
Mapped : 66096436 (97.2% of input)
...
Forum: Bioinformatics 11-18-2013, 12:05 PM
Replies: 1
Views: 1,072
Posted By Starr_Hazard
Chimerscan 0.4.5 runs for days and then system kills it

https://code.google.com/p/chimerascan/

I have some paired read files that range from 1.8Gb to just under 3.0Gb.
Chimerascan works on the smallish test files distributed with the software....
Forum: Bioinformatics 04-10-2013, 01:11 PM
Replies: 18
Views: 4,402
Posted By Starr_Hazard
CuffDiff Threads vs Processes

Folks,
I am trying to run a CuffDiff analysis as indicated below. There are 19 single-end read files and I am trying an all-vs-all comparison because that is something the users wish to know.
The...
Forum: Bioinformatics 03-19-2013, 08:33 AM
Replies: 0
Views: 1,451
Posted By Starr_Hazard
CuffDiff tries to get 23G swap and is killed

Folks

I am having trouble getting a CuffDiff run to successfully complete. It runs
24-28 hours then gets killed by my LSF scheduler with an exit code of 137
which translates to 9 or job memory...
Forum: Bioinformatics 01-28-2013, 08:22 AM
Replies: 1
Views: 1,697
Posted By Starr_Hazard
Anyone built an iGenome index for RN5

Igenome and BOWTIE prebuilt indexes both list RN4.
(Rat version4 )

Researchers here want to be certain that their NGS data is aligned to the latest and greatest.

UCSC Genome Browser allows...
Forum: Bioinformatics 08-24-2012, 08:34 AM
Replies: 3
Views: 1,460
Posted By Starr_Hazard
CuffDiff and Significant Splicing events

Folks,

We are looking at RNASeq data from rat brain.
The experimental protocol is to compare sham (or S: saline treated) versus experimental (or C: chemical treated).
Several pairs of animals...
Forum: RNA Sequencing 06-20-2012, 01:26 PM
Replies: 61
Views: 34,502
Posted By Starr_Hazard
Reading in a table of Gene names for cummeRbund analysis

I want examine the CuffDiff/cummeRbund analyses for a list of genes that other RNAseq software has flagged as significant for my data.

I made both plain text and csv tables of the gene names ...
Forum: Bioinformatics 05-08-2012, 06:56 AM
Replies: 9
Views: 2,782
Posted By Starr_Hazard
Thanks again Loyal. That's just the sort of...

Thanks again Loyal. That's just the sort of child's primer for relating SQLite and cummeRbund that I have been looking for
Forum: Bioinformatics 04-27-2012, 11:05 AM
Replies: 9
Views: 2,782
Posted By Starr_Hazard
cummeRbund ANDing in getSig

Folks,

getSig can select a set based on alpha level eg

mySigGenes<-getSig(cuff,x='Control',y='Experiment',alpha=0.01,level='genes')

Is there a way to get alpha=0.01 AND ,say, FPKM greater or...
Forum: Bioinformatics 04-25-2012, 09:15 AM
Replies: 0
Views: 1,609
Posted By Starr_Hazard
Plotting cuffdiff TCONS_### as glyphs

Folks,

In figure 10a of the Trapnell et al 2012 Nature Protocol paper the authors display a series of four TCONS_### entries as a series of "exon glyphs"

It seems to me that this is a useful...
Forum: Bioinformatics 04-24-2012, 09:43 AM
Replies: 33
Views: 34,338
Posted By Starr_Hazard
OK so plotting routine fails on the gene AFTER...

OK so plotting routine fails on the gene AFTER the last one in the output
When I run the commands outside of the loop here's what happens

> library(cummeRbund)
Loading required package: RSQLite...
Forum: Bioinformatics 04-23-2012, 08:39 AM
Replies: 33
Views: 34,338
Posted By Starr_Hazard
So now I can get gene_short_names from...

So now I can get gene_short_names from significant TSS ids-- I just cannot plot them

The plot commands I am using are straight out of the cummeRbund manual except that I put them into a for-next...
Forum: Bioinformatics 04-21-2012, 06:09 AM
Replies: 33
Views: 34,338
Posted By Starr_Hazard
So, I figured out the issues of getting isoforms...

So, I figured out the issues of getting isoforms data plotted like I want but I now see and issue with duplicate entries AND have a general question

Why do the plotting programs fail when told to...
Forum: Bioinformatics 04-19-2012, 02:26 PM
Replies: 33
Views: 34,338
Posted By Starr_Hazard
I am in a similar fix and I am a cummeRbund...

I am in a similar fix and I am a cummeRbund newbie too.

I am running R-2.15.2 and the BioConductor loaded cummeRbund so as of the first of the month I am mostly up-to-date.

What I want to do is...
Forum: Bioinformatics 03-22-2012, 01:38 PM
Replies: 4
Views: 1,493
Posted By Starr_Hazard
Perfect. Thanks.

Perfect. Thanks.
Forum: Bioinformatics 03-22-2012, 08:13 AM
Replies: 4
Views: 1,493
Posted By Starr_Hazard
awk editing, and bowtie indexing not really working to help

I looked at my ebwt index with bowtie and indeed it uses "chr" prefixes for all
chromosomes. (eg chr1,chrX,chrM,chrUn,,,, etc)

The ENSEMBL GTF file references all chromosomes without the "chr"...
Forum: Bioinformatics 12-02-2011, 12:28 PM
Replies: 4
Views: 1,493
Posted By Starr_Hazard
CuffDiff Question

Here's a line from a CuffDiff output (v 1.2.0) where I had used tophat and the -g (RABT option) and supplied an annotation gtf file.

TCONS_00039273 XLOC_029459 Rpl10 X:160336635-160338842 ...
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