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Forum: Bioinformatics 04-10-2015, 07:44 AM
Replies: 4
Views: 7,638
Posted By bpb9
I'm also struggling with the syntax of the design...

I'm also struggling with the syntax of the design formula. I want to identify genes differentially expressed between two ancestries of two health statuses at each of 4 time points. I'm not sure if I...
Forum: RNA Sequencing 01-20-2015, 05:31 PM
Replies: 10
Views: 6,302
Posted By bpb9
Pull Principal Components from DESeq plotPCA

#Load libraries
library(gplots)
library(RColorBrewer)
library(lattice)
library(genefilter)

#Define the plotPCA function
plotPCA4<-function (x, intgroup = "condition", ntop = 500)
{
rv...
Forum: RNA Sequencing 11-25-2014, 11:17 PM
Replies: 36
Views: 15,117
Posted By bpb9
You are correct, there is indeed output for...

You are correct, there is indeed output for unmapped_fixup.bam but not unmapped.bam.

I still think it's really weird that there are no duplicates in the unmapped file, but that must be a separate...
Forum: Bioinformatics 11-25-2014, 10:19 PM
Replies: 5
Views: 4,998
Posted By bpb9
I came across this lovely thing:...

I came across this lovely thing: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/faq.html

"Outliers in expression data are usually harder to deal with. The accepted remedy by the...
Forum: RNA Sequencing 11-25-2014, 09:29 PM
Replies: 36
Views: 15,117
Posted By bpb9
So it got it to run if I stayed in the same...

So it got it to run if I stayed in the same directory as tophat-recondition.py and removed -hv command, and pointed it to the tophat output directories. I think the reason why is because on the...
Forum: RNA Sequencing 11-25-2014, 03:12 PM
Replies: 36
Views: 15,117
Posted By bpb9
How to use?

Does this program need to be installed in the same directory as the unmapped bams that need to be reconditioned? I can't seem to get the program to work. I have python and pysam installed, but the...
Forum: Bioinformatics 11-24-2014, 10:57 PM
Replies: 5
Views: 4,998
Posted By bpb9
I have what is probably a naive question about...

I have what is probably a naive question about DESeq normalization. The manual says that by dividing the count by the size factor, one makes samples comparable. Does this include comparable for, say,...
Forum: RNA Sequencing 11-23-2014, 01:56 AM
Replies: 10
Views: 6,302
Posted By bpb9
I am able to change the colors by modifying the...

I am able to change the colors by modifying the plotPCA function (check out ?brewer.pal to see the options for colors--there are several color schemes if you don't like "paired"). Or you can just...
Forum: Bioinformatics 11-21-2014, 05:38 AM
Replies: 17
Views: 23,985
Posted By bpb9
Hi Simon, by cdsFilt I mean I did the following: ...

Hi Simon, by cdsFilt I mean I did the following:

cdsFilt:

rs <- rowSums ( counts ( cds ))
use <- (rs > quantile(rs, 0.4))
table(use)
FALSE TRUE
10,000 15,243
#Proceed with...
Forum: Bioinformatics 11-20-2014, 06:46 PM
Replies: 17
Views: 23,985
Posted By bpb9
When I run DESeq and look at my dispersion...

When I run DESeq and look at my dispersion estimates verus normalized expression, it seems that most genes have either very low or very high read counts even after normalization. I am normalizing...
Forum: Bioinformatics 11-16-2014, 05:53 PM
Replies: 4
Views: 2,917
Posted By bpb9
Discrepancy between Tophat align_summary and samtools flagstat paired end

I also used TopHat2 to align 50bp paired-end reads. I used the --no-mixed option in TopHat and then compared align_summary.txt to samtools flagstat. The numbers are not identical but they are not as...
Forum: RNA Sequencing 10-16-2014, 04:43 AM
Replies: 10
Views: 8,716
Posted By bpb9
Warning can be ignored

Hm…sure enough, despite the warning, there is in fact a fastq file produced anyway.

But when I run the program from the cluster's login node (shame on me, I know) I don't get the error, and I...
Forum: Bioinformatics 10-15-2014, 02:33 PM
Replies: 20
Views: 5,945
Posted By bpb9
libz warning?

dpryan, how does one ignore the libz warning? I got that warning while trying to use bam2fastx from top hat 2.0.9...
Forum: RNA Sequencing 10-15-2014, 12:08 PM
Replies: 10
Views: 8,716
Posted By bpb9
bam2fastx libz error

I too am trying to make a fast file out of the unmapped reads so that I can run top hat on an alternative genome. I get a different error:

samtools sort -n unmapped.bam unmapped_sort.bam...
Forum: Bioinformatics 02-19-2013, 11:10 AM
Replies: 10
Views: 10,021
Posted By bpb9
After having made the plink files from the VCF...

After having made the plink files from the VCF file, I tried to split them up by chromosome in plink but encountered the following error:

ERROR: Locus has >2 alleles:
individual has...
Forum: Bioinformatics 02-19-2013, 05:05 AM
Replies: 10
Views: 10,021
Posted By bpb9
Thanks for the tips!

Thanks for the tips!
Forum: Bioinformatics 02-19-2013, 04:16 AM
Replies: 10
Views: 10,021
Posted By bpb9
I am also trying to convert a VCF file to plink...

I am also trying to convert a VCF file to plink format using vcftools, but the process never seems to result in a plink file. For example when I enter:

./vcftools --vcf filename.vcf --plink

I...
Forum: Bioinformatics 10-02-2012, 11:03 AM
Replies: 13
Views: 5,697
Posted By bpb9
Nevermind, I've just answered my own question, I...

Nevermind, I've just answered my own question, I think. Clicking on Petr's link above (ftp://ftp.1000genomes.ebi.ac.uk/vol1...ral_alignments), there is a readme.ancestralalignments txt file in the...
Forum: Bioinformatics 10-02-2012, 10:21 AM
Replies: 13
Views: 5,697
Posted By bpb9
Anyone know what the "-" and "." mean in fill-aa?

I used the fill-aa feature in vcf tools to pull the ancestral alleles, according to thousand genomes, for variants I have typed in another population. However, I did not get an ancestral allele call...
Forum: Bioinformatics 08-10-2012, 09:58 AM
Replies: 15
Views: 8,788
Posted By bpb9
Dong, it appears that program is only for Windows...

Dong, it appears that program is only for Windows users.

Kennels, your way was SO much faster! Thanks!
Forum: Bioinformatics 08-10-2012, 09:51 AM
Replies: 15
Views: 8,788
Posted By bpb9
Thanks for the tips. I will definitely try this...

Thanks for the tips. I will definitely try this and let you know how it goes. I ended up using R yesterday to do this, but it took about an hour just to read in the file. After that I was able to...
Forum: Introductions 08-09-2012, 08:44 AM
Replies: 5
Views: 1,553
Posted By bpb9
Thanks!

Thanks everyone. I will definitely scour the web and program documentation and attempt things on my own before posting!
Forum: Bioinformatics 08-09-2012, 06:55 AM
Replies: 15
Views: 8,788
Posted By bpb9
Split VCF by chromosome?

Hello, I am also new to the world of genomic datasets, tabix and vcf files. I understand that vcf files are basically giant text files, however due to their size I am unable to open them. I was able...
Forum: Introductions 08-08-2012, 05:56 AM
Replies: 5
Views: 1,553
Posted By bpb9
Please don't eat me.

Hello SeqAnswers community! Very glad to have found this forum. I apologize in advance for asking what to some might be obvious questions, but having recently made the switch from bench to desktop, I...
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