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Search: Posts Made By: dmacmillan
Forum: Bioinformatics 02-15-2016, 11:03 AM
Replies: 5
Views: 1,561
Posted By dmacmillan
Interesting, glad I know this now. Thanks!

Interesting, glad I know this now. Thanks!
Forum: Bioinformatics 02-15-2016, 10:58 AM
Replies: 5
Views: 1,561
Posted By dmacmillan
Well the distance from that read to the actual...

Well the distance from that read to the actual start location is ~280,000 nucleotides. I suppose then the read would have to be spliced? Here is one of the reads in question:

...
Forum: Bioinformatics 02-15-2016, 09:02 AM
Replies: 5
Views: 1,561
Posted By dmacmillan
Pysam Fetching Incorrect Coordinates

Hello everyone. I am using pysam (https://github.com/pysam-developers/pysam) to fetch the reads overlapping a given region, however, I am finding that pysam returns a list of reads whose positions do...
Forum: De novo discovery 07-03-2012, 09:25 AM
Replies: 1
Views: 1,725
Posted By dmacmillan
Oases Help

I get an error when trying to do the final merge stage of oases. This is my command and output:

../assemblers/oases_0.2.07_x11/oases MergedAssembly/ -merge yes

[0.000000] Reading graph file...
Forum: De novo discovery 05-11-2012, 08:37 AM
Replies: 5
Views: 2,885
Posted By dmacmillan
Yes sorry I forgot to mention I tried the...

Yes sorry I forgot to mention I tried the obvious, setting the stacksize to unlimited did not solve the problem.
Forum: De novo discovery 05-10-2012, 12:21 PM
Replies: 5
Views: 2,885
Posted By dmacmillan
Trinity Help

So I ran trinity, but I am experiencing this error:

Error, the Chrysalis process failed:
Error, cmd: /projects/dmacmillanprj2/assembly/trinityrnaseq_r2012-04-27/Chrysalis/Chrysalis -i both.fa...
Forum: De novo discovery 05-08-2012, 10:14 AM
Replies: 5
Views: 2,707
Posted By dmacmillan
Oh I see, I did have another question. How do you...

Oh I see, I did have another question. How do you get the insert length and expected coverage for paired-end reads? I have a bunch of fastq files I downloaded from NCBI.
Forum: De novo discovery 05-04-2012, 03:46 PM
Replies: 5
Views: 2,707
Posted By dmacmillan
I found the solution, you simply do make...

I found the solution, you simply do

make 'MAXKMERLENGTH=92'

or whatever when you compile velvet and oases. Good luck!
Forum: De novo discovery 05-04-2012, 03:13 PM
Replies: 5
Views: 2,707
Posted By dmacmillan
Oases Question

So I am analyzing strand-specific RNA seq data of Schizosaccharomyces pombe using Oases v0.2.06

I used ABySS to create kmer values of 34,36,38,...,64. When I try to use oases with a value > 31 I...
Forum: Bioinformatics 04-30-2012, 03:28 PM
Replies: 2
Views: 1,834
Posted By dmacmillan
I would be interested in finding some...

I would be interested in finding some strand-specific RNA-Seq data that is publicly available as well!
Forum: Bioinformatics 04-26-2012, 03:50 PM
Replies: 11
Views: 8,763
Posted By dmacmillan
Interesting tips, I will try both, thanks!

Interesting tips, I will try both, thanks!
Forum: Bioinformatics 04-26-2012, 10:01 AM
Replies: 11
Views: 8,763
Posted By dmacmillan
I understand what you are doing here, but what is...

I understand what you are doing here, but what is with the '-;' at the end (ignoring the single quotations)?
Forum: Bioinformatics 04-20-2012, 04:04 PM
Replies: 11
Views: 8,763
Posted By dmacmillan
BWA sampe to bam?

So as everyone who uses bwa knows, the sampe function outputs a file in sam format. What I want to do is somehow convert that sam file to a bam file in some sort of pipe? It seems easy to implement,...
Forum: Literature Watch 02-29-2012, 12:06 PM
Replies: 76
Views: 43,132
Posted By dmacmillan
Oh I forgot to ask about the circos format...

Oh I forgot to ask about the circos format script. I plugged in my *ratios.txt file and got some output. But it does not look like circos format to me, how am I supposed to use the output given from...
Forum: Literature Watch 02-29-2012, 10:35 AM
Replies: 76
Views: 43,132
Posted By dmacmillan
No I currently do not, to save time. I will try...

No I currently do not, to save time. I will try it with the GEM file though. I'll let you know how it goes!
Forum: Literature Watch 02-29-2012, 10:18 AM
Replies: 76
Views: 43,132
Posted By dmacmillan
Yes this helps. I was also wondering if there was...

Yes this helps. I was also wondering if there was a way to smooth out centromere calls? It seems to call very high or very short CNVs nearing centromeres.
Forum: Literature Watch 02-27-2012, 09:38 AM
Replies: 76
Views: 43,132
Posted By dmacmillan
Hi, so I have been using this software for...

Hi, so I have been using this software for multiple analyses. However there are some quirks.

Here is a template of my config file:

[general]

chrLenFile =...
Forum: Literature Watch 02-10-2012, 01:34 PM
Replies: 76
Views: 43,132
Posted By dmacmillan
I managed to find out what file you were using,...

I managed to find out what file you were using, it turns out it is under tables > your assembly > all tracks > SNP130 (if your using hg18, for hg19 its 131) > hg18.snp130OrthoPt2Pa2Rm2

You then...
Forum: Literature Watch 02-09-2012, 02:32 PM
Replies: 76
Views: 43,132
Posted By dmacmillan
Could you be more specific? I have looked at the...

Could you be more specific? I have looked at the tables and gone through a lot of SNP's but none of them match the formatting of the file you include on the tutorial page where it gives the...
Forum: Bioinformatics 02-09-2012, 08:37 AM
Replies: 25
Views: 20,082
Posted By dmacmillan
Good to know, thanks for the input!

Good to know, thanks for the input!
Forum: Literature Watch 02-08-2012, 01:37 PM
Replies: 76
Views: 43,132
Posted By dmacmillan
Could you point out where you found it? When I...

Could you point out where you found it? When I look at hg18 downloads all I see are fasta files corresponding to SNPs.
Forum: Literature Watch 02-08-2012, 10:27 AM
Replies: 76
Views: 43,132
Posted By dmacmillan
Thank you for the reply, that is helpful to know....

Thank you for the reply, that is helpful to know.

Another question,
How would one go about getting or creating a text file with SNPs such as the one you provide on the website? So as to use the...
Forum: Literature Watch 02-07-2012, 02:49 PM
Replies: 76
Views: 43,132
Posted By dmacmillan
I have a couple questions about Control-FREEC, ...

I have a couple questions about Control-FREEC,


How does it use the normal sample if provided?
If one provides a normal sample as well as chromosome fasta files, does it account for gc-content...
Forum: Bioinformatics 02-02-2012, 03:25 PM
Replies: 2
Views: 3,431
Posted By dmacmillan
It was designed for the human genome yes.

It was designed for the human genome yes.
Forum: Bioinformatics 02-02-2012, 02:28 PM
Replies: 2
Views: 3,431
Posted By dmacmillan
Split up a Bam file with chrom-bed

I saw a couple posts, not specifically here but elsewhere that asked how one could divide a "bam" file into certain chunks or into its individual chromosomes. Well while working with readDepth I...
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