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Forum: Bioinformatics 10-11-2017, 11:19 AM
Replies: 2
Views: 708
Posted By aprice67
If you are using a cluster or SGE setup, you...

If you are using a cluster or SGE setup, you might try to qlogin and see if you can still find the files and if the paths are correct. You might check if the permissions on those input files are...
Forum: Bioinformatics 10-11-2017, 11:07 AM
Replies: 1
Views: 584
Posted By aprice67
Simulome might do it. Put both parent genomes...

Simulome might do it. Put both parent genomes into a single fasta, then use that as a base for randomly simulating a single genome that would be the same size as an individual genome.
...
Forum: Bioinformatics 09-07-2017, 12:43 PM
Replies: 1
Views: 518
Posted By aprice67
Hi, I have a script that does that from my...

Hi,

I have a script that does that from my PhD days. I actually used this for some RNA secondary structure projects, so it looks like you're working on something similar.
...
Forum: Bioinformatics 09-07-2017, 12:01 PM
Replies: 2
Views: 581
Posted By aprice67
First thing I'd try is throwing a ton of memory...

First thing I'd try is throwing a ton of memory at it. See if it runs with 64G of memory. If it does maybe slim it down for other jobs. Segmentation faults say to me that the problem has something...
Forum: Bioinformatics 08-28-2017, 09:20 AM
Replies: 1
Views: 495
Posted By aprice67
Have you tried running it on a different machine?...

Have you tried running it on a different machine? Maybe its a configuration issue.
Forum: Bioinformatics 08-28-2017, 09:14 AM
Replies: 1
Views: 462
Posted By aprice67
I'm not sure exactly what you are doing, you...

I'm not sure exactly what you are doing, you might want to provide more information about your experiment.

You also might look into the Lapels and Suspenders pipeline...
Forum: Bioinformatics 08-23-2017, 06:43 AM
Replies: 7
Views: 871
Posted By aprice67
Be very careful when dealing with MAPQ scores. ...

Be very careful when dealing with MAPQ scores. It seems every aligner has a different way to determine them and they aren't standardized at all. See here:
...
Forum: Bioinformatics 08-22-2017, 01:14 PM
Replies: 7
Views: 871
Posted By aprice67
Check out figure 12 and the area around it in...

Check out figure 12 and the area around it in this paper.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180904

It might not be such a good idea to remove them.
Forum: Bioinformatics 08-22-2017, 12:38 PM
Replies: 6
Views: 974
Posted By aprice67
Basically, to sum up, it's okay to use a...

Basically, to sum up, it's okay to use a non-native reference of a closely related strain as long as your reads are pretty long. Reads of 100bp do pretty well, 150 do great, 50 are bad. When you...
Forum: Bioinformatics 08-22-2017, 11:36 AM
Replies: 0
Views: 712
Posted By aprice67
Question How can I make a valid design for this data in DESeq2?

So I have a problem with a dataset I'm working on. Here is information about the samples.

Three viruses at three timepoints:
Virus1_day1, Virus1_day3, Virus1_day8.
Virus2_day1, Virus2_day3,...
Forum: Bioinformatics 08-22-2017, 11:21 AM
Replies: 6
Views: 974
Posted By aprice67
I recently published a paper on this exact topic....

I recently published a paper on this exact topic. It show how alignment to non-native reference genomes influences outcomes and gives best practices for doing it. I used an e-coli data set in here...
Forum: Bioinformatics 06-20-2017, 07:21 AM
Replies: 7
Views: 1,743
Posted By aprice67
As someone on the other side of the fence, let me...

As someone on the other side of the fence, let me assure you the grass is not quite so green as you might think. Maybe i'd rather have the weird fish. At least then I can say the annotation is to...
Forum: Bioinformatics 06-20-2017, 07:07 AM
Replies: 7
Views: 1,743
Posted By aprice67
That's a very nice thing to know, thanks for...

That's a very nice thing to know, thanks for pointing this out. I feel slightly safer now. I wonder, are you working with mouse data as well?
Forum: Bioinformatics 06-20-2017, 06:41 AM
Replies: 7
Views: 1,743
Posted By aprice67
That might be one contributing factor, but it's...

That might be one contributing factor, but it's not enough to explain the scale of the read loss, at least not in my data. The level of multi-mapped reads I'm seeing is something on average of...
Forum: Bioinformatics 05-26-2017, 07:35 AM
Replies: 3
Views: 645
Posted By aprice67
Samtools sort will produce a sorted bam file and...

Samtools sort will produce a sorted bam file and a .bam.bai file to go with it.

For example,
samtools sort bam_unsorted.bam > myBam_sorted.bam

That will make: myBam_sorted.bam and...
Forum: Bioinformatics 05-26-2017, 07:17 AM
Replies: 1
Views: 495
Posted By aprice67
Can prinseq do trim_left on paired-end?

When using prinseq on paired end data and I want to trim the 5' end of both reads by 10 bases, how can I do it?

I've tried -trim_left 10 because I assumed it would do the same for both. Maybe...
Forum: Bioinformatics 05-25-2017, 01:46 PM
Replies: 2
Views: 856
Posted By aprice67
I'm not sure what you'll have to do to get your...

I'm not sure what you'll have to do to get your data, but I can give you some advice on the RNA-seq part.

If you're starting with BAM files that means your reads are already aligned, if you start...
Forum: Bioinformatics 05-25-2017, 12:19 PM
Replies: 0
Views: 658
Posted By aprice67
Question Cuffset number of genes too high

Hi,

So I'm implementing a pretty standard tuxedo pipeline on paired-end mouse data. I went along as follows.

Using the standard mouse build (37) from Ensemble and the associated annotation...
Forum: Bioinformatics 05-17-2017, 02:13 PM
Replies: 7
Views: 1,743
Posted By aprice67
Large number of Unassigned_NoFeature reads from featureCounts

I have a bit of a mystery on my hands about an RNA-Seq Project.

I am working with some mice lines, standard RNA-seq prep, paired end. Initial adapter trimming is done with cutadapt. At this point...
Forum: Bioinformatics 07-25-2016, 12:20 PM
Replies: 6
Views: 1,411
Posted By aprice67
Bowtie2. I also think it's pretty high. It's a...

Bowtie2. I also think it's pretty high. It's a publicly available dataset I found through a paper. As far as I know reads are all the same length.
Forum: Bioinformatics 07-25-2016, 12:02 PM
Replies: 6
Views: 1,411
Posted By aprice67
So I have some real datasets and I'm looking at...

So I have some real datasets and I'm looking at false discovery of differentially expressed genes. I'm particularly looking at how using closely related reference genomes (but not exactly the one...
Forum: Bioinformatics 07-25-2016, 10:34 AM
Replies: 6
Views: 1,411
Posted By aprice67
I want to show if different levels of reads...

I want to show if different levels of reads mapping to multiple locations has a specific effect in a very controlled way. I could go and find a bunch of different genomes and simulate rna seq reads...
Forum: Bioinformatics 07-25-2016, 09:51 AM
Replies: 6
Views: 1,411
Posted By aprice67
Simulating a prokaryotic genome

I want to simulate a genome, then simulate RNA-seq reads from that genome that will map with varying degrees of multi-mapping. So for instance, I want 10% of reads to map more than once, 20% of...
Forum: Bioinformatics 07-21-2016, 01:24 PM
Replies: 1
Views: 919
Posted By aprice67
Question Identifying paralogs for a whole genome

I have an e. coli genome and I want to know which genes are paralogs so I can investigate how RNA-seq reads are mapping to multiple positions. What I would like to do is get a full list of paralogs...
Forum: Bioinformatics 06-23-2016, 10:19 AM
Replies: 1
Views: 694
Posted By aprice67
Question Bowtie2 and differences in read counts. How can this be?

So I have some RNA-seq data for prokaryotes. Lets say I have strain A and strain B, and for each I have two replicates and two conditions. I want to do differential expression on these.

Now, if...
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