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Forum: Bioinformatics 01-07-2015, 01:49 PM
Replies: 17
Views: 2,435
Posted By Wallysb01
BLAT is really the wrong tool for short reads (at...

BLAT is really the wrong tool for short reads (at least without careful tuning of parameters and post filtering), especially if the goal is to decide where these reads are actually coming from. By...
Forum: General 11-13-2014, 09:18 PM
Replies: 3
Views: 1,334
Posted By Wallysb01
use abyss-pe, but only in single end mode, i.e.: ...

use abyss-pe, but only in single end mode, i.e.:



$ABYSS_DIR/abyss-pe n=5 k=21 name=K27ac np=12 s=50 se='K27ac_rep1.fastq K27ac_rep2.fastq' > out.txt
Forum: General 11-11-2014, 01:20 PM
Replies: 3
Views: 1,334
Posted By Wallysb01
I’m not sure why you’d want to use trinity, since...

I’m not sure why you’d want to use trinity, since its set up to try to find splice forms. You could just use the inchworm assembly though I suppose.

I’ve played around with de novo ChIPseq and...
Forum: RNA Sequencing 11-07-2014, 08:25 AM
Replies: 2
Views: 919
Posted By Wallysb01
You should read up on the interaction terms and...

You should read up on the interaction terms and changing the comparisons when you call the results function.

The design probably needs to look something like:

design ~ genotype + sex + inf_type...
Forum: Sample Prep / Library Generation 11-07-2014, 08:18 AM
Replies: 5
Views: 1,407
Posted By Wallysb01
Your input has a lot of really big chromatin...

Your input has a lot of really big chromatin fragments in it still (7-17, 9-14) or its very short with a odd curve shape overall (8-14). It would seem you still need to optimize the sheering and...
Forum: Sample Prep / Library Generation 11-06-2014, 11:58 AM
Replies: 5
Views: 1,407
Posted By Wallysb01
Its hard to say what could be going on from what...

Its hard to say what could be going on from what information you gave. Maybe you’re over amplifying, maybe you have far more or far less starting material than you think? Do you have bioanalyzer...
Forum: Bioinformatics 10-15-2014, 07:47 AM
Replies: 8
Views: 1,861
Posted By Wallysb01
Yeah, it would be nice to clarify the question of...

Yeah, it would be nice to clarify the question of how many people are expected to simultaneously use this thing. When you said it was for a whole department, I assumed we might be talking about a...
Forum: Bioinformatics 10-15-2014, 07:43 AM
Replies: 8
Views: 1,861
Posted By Wallysb01
A small cluster with at least one high memory...

A small cluster with at least one high memory node is probably what would be most efficient if you’re talking about whole department with very different tasks.

If it were me I’d maybe look at...
Forum: Bioinformatics 10-09-2014, 08:30 AM
Replies: 20
Views: 7,019
Posted By Wallysb01
I second GenoMax, if you’re not particularly...

I second GenoMax, if you’re not particularly computationally inclined, managing your own workstation is maybe more than you should try to do.

Often what is possible is that you buy a computer (it...
Forum: Bioinformatics 10-08-2014, 02:58 PM
Replies: 6
Views: 867
Posted By Wallysb01
Wouldn't this then mean that you could call hets,...

Wouldn't this then mean that you could call hets, and called hets are very likely hets, but homozygous calls could be hets? So that with het calling, its more the false negative rate that causes the...
Forum: Bioinformatics 09-04-2014, 11:23 AM
Replies: 18
Views: 4,424
Posted By Wallysb01
Brain's comments above about core count vs clock...

Brain's comments above about core count vs clock speed in bioinformatics should help you guage how worth it each CPU upgrade might be. If you're doing a lot of aligning, maximizing core count * GHz...
Forum: Bioinformatics 09-04-2014, 08:52 AM
Replies: 18
Views: 4,424
Posted By Wallysb01
One other quick suggestion, Supermicro...

One other quick suggestion, Supermicro motherboards and cases are really nice. That case you have picked out looks pretty slick, but it will probably get cramped with a duel LGA 2011 motherboard and...
Forum: Bioinformatics 09-04-2014, 08:28 AM
Replies: 18
Views: 4,424
Posted By Wallysb01
I think you’ve absolutely made the right choice...

I think you’ve absolutely made the right choice going with the 2x2650s. A couple of suggestions though:

1) Don’t get seagate drives. I just have 2 out of 5 of them start accumulating bad sectors....
Forum: Bioinformatics 08-28-2014, 10:08 AM
Replies: 22
Views: 3,564
Posted By Wallysb01
I have to agree, don’t go with some...

I have to agree, don’t go with some 'pre-packaged’ commercial software and don’t buy a workstation from them. You’ll get ripped off on the hardware and the software from those places tends to be...
Forum: Bioinformatics 08-20-2014, 03:11 PM
Replies: 14
Views: 3,667
Posted By Wallysb01
since htseq is always going to be in the same...

since htseq is always going to be in the same order, I just use paste (which can takes a space seperated list of your files) and awk. Paste will print the row names for each file, so that's what awk...
Forum: Bioinformatics 08-18-2014, 02:23 PM
Replies: 4
Views: 1,742
Posted By Wallysb01
It sounds messy to me to have 5 wiggles (or 10)...

It sounds messy to me to have 5 wiggles (or 10) overlaid. In my experience this is hard to interpret. I would personally just average the wiggle files and have test and control tracks separated. Its...
Forum: Bioinformatics 08-13-2014, 04:07 PM
Replies: 3
Views: 2,016
Posted By Wallysb01
Just get the binaries instead of the source code

Just get the binaries instead of the source code
Forum: Sample Prep / Library Generation 07-24-2014, 07:20 AM
Replies: 4
Views: 1,243
Posted By Wallysb01
I’ve had good results with the miRVana kit.

I’ve had good results with the miRVana kit.
Forum: Bioinformatics 07-22-2014, 07:45 AM
Replies: 14
Views: 1,900
Posted By Wallysb01
Hum, looks like you’ve type “spilt” when you mean...

Hum, looks like you’ve type “spilt” when you mean “split”.

You could also convert you fasta file into tab format then just use a join command. Ie it could be:

File1:

someheader1 GATC…....
Forum: Bioinformatics 07-22-2014, 07:31 AM
Replies: 9
Views: 1,080
Posted By Wallysb01
I suppose what you might be looking for is IGV,...

I suppose what you might be looking for is IGV, it does a very nice job of displaying coverage coming from an aligned bam file. It can show you things like SNPs/indels in your reads too.
Forum: Bioinformatics 07-21-2014, 01:06 PM
Replies: 8
Views: 3,342
Posted By Wallysb01
Are you trying to compile it from source and...

Are you trying to compile it from source and getting errors or are you just trying the provided binaries and they aren’t working?

If you’re trying to compile it, I’d suggest you try the binaries...
Forum: Bioinformatics 07-18-2014, 07:35 AM
Replies: 1
Views: 1,042
Posted By Wallysb01
If all you’re going for is an accurate FPKM, why...

If all you’re going for is an accurate FPKM, why not just use cufflinks, which assigns FPKMs based on a most likely explanation of the reads method rather than some non-overlapping business gene...
Forum: Bioinformatics 07-16-2014, 10:44 AM
Replies: 2
Views: 710
Posted By Wallysb01
If you ran maker on just the contigs of your...

If you ran maker on just the contigs of your genome assembly and now you have scaffolds, you should rerun maker from the beginning on those scaffolds. Trying some sort of liftover of your gff file is...
Forum: Bioinformatics 07-11-2014, 10:52 AM
Replies: 6
Views: 1,067
Posted By Wallysb01
The basic idea here is you’re looking for genes...

The basic idea here is you’re looking for genes in which the beta term in the equation expression = beta * stage + constant is significantly different from zero. This is a generalized linear model. ...
Forum: RNA Sequencing 07-07-2014, 09:14 PM
Replies: 2
Views: 1,122
Posted By Wallysb01
Is this RT-qPCR on the same RNA that was...

Is this RT-qPCR on the same RNA that was sequenced?

What was the ct-value for the gene?

How many reads did get for this sample?

There is going to be a pretty big difference between...
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