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Search: Posts Made By: rndouglas
Forum: Bioinformatics 07-29-2015, 04:41 AM
Replies: 4
Views: 2,584
Posted By rndouglas
For me, it was an issue with IGV. When I looked...

For me, it was an issue with IGV. When I looked more closely IGV was coloring nucleotides as being mismatched, but they really were not mismatched. I never found a workaround/explanation, so I just...
Forum: De novo discovery 08-20-2014, 11:30 AM
Replies: 0
Views: 1,519
Posted By rndouglas
miRNA Discovery

I may be a bit naive, but I'm trying to see if I can identify miRNA-precursors in a new genome assembly I recently made.

I have available to me:

de novo assembled genome
1x100bp Illumina...
Forum: Bioinformatics 07-15-2014, 07:57 AM
Replies: 0
Views: 1,264
Posted By rndouglas
Masurca ignoring input FASTA

I have been trying to assemble some sequences using Masurca, and it runs to completion, but I recently noticed something amiss.

For input, I have three paired-end Illumina libraries, three...
Forum: Bioinformatics 11-08-2013, 05:54 AM
Replies: 5
Views: 1,666
Posted By rndouglas
I just realized I'm only seeing this in my...

I just realized I'm only seeing this in my smallRNA libraries (adapter removed, t/rRNA removed, size-selected for 20-25nt in sRNA Workbench).

I map the reads using bowtie (-v 0).

I generate...
Forum: Bioinformatics 11-07-2013, 10:59 AM
Replies: 5
Views: 1,666
Posted By rndouglas
This is what I had been doing all along (running...

This is what I had been doing all along (running everything in one count table), but then this morning I thought I'd try A vs. B in a separate count table.

I was surprised to find almost double...
Forum: Bioinformatics 11-07-2013, 08:02 AM
Replies: 5
Views: 1,666
Posted By rndouglas
What to include in my count table(s) for DESeq

I have five experimental groups (A, B, C, D, and E; 3-6 bioreps each) that I want to compare to each other and a control (Y; 3 bioreps) using DESeq.

When I run DESeq is it better to use a count...
Forum: Bioinformatics 08-22-2013, 01:32 PM
Replies: 5
Views: 3,066
Posted By rndouglas
Thanks for all the help! So far, I've had luck by...

Thanks for all the help! So far, I've had luck by splitting my input files in half, correcting my input code, and finding a machine with much more memory for my runs.
Forum: Bioinformatics 08-19-2013, 05:53 AM
Replies: 5
Views: 3,066
Posted By rndouglas
Thank you very much for the suggestion! I'll...

Thank you very much for the suggestion! I'll start looking into that right away.
Forum: Bioinformatics 08-19-2013, 05:32 AM
Replies: 5
Views: 3,066
Posted By rndouglas
Velvet killed

I am trying to run velveth with paired-end, fastq files for a de novo genome assembly, but after running ~18 hours (16 CPU, 32 GB RAM) my runs end with just "Killed"

I've tried k-mers from 29 up...
Forum: Sample Prep / Library Generation 11-29-2012, 08:59 AM
Replies: 29
Views: 7,955
Posted By rndouglas
As an update... I FINALLY received some of...

As an update...

I FINALLY received some of my rRNA-depleted samples back from our DNA core this week.

They look pretty good, and they have almost no rRNA present. The first two samples came...
Forum: Bioinformatics 11-09-2012, 07:59 AM
Replies: 4
Views: 2,584
Posted By rndouglas
Cranking up the frustration a notch.... This...

Cranking up the frustration a notch....

This week I discovered the same situation (up to 20 mismatches on a 24 nt "mapped" read) occurs when I set -v to 0, supposedly not allowing for mismatches....
Forum: Bioinformatics 11-05-2012, 05:56 AM
Replies: 4
Views: 2,584
Posted By rndouglas
Bowtie mapping with more than 3 mismatches?

I'm trying to map some sRNA reads to specific loci of interest while allowing up to 3 mismatches using -v 3.

For some of my target loci, this seems to work well. All of the mapped reads have no...
Forum: Bioinformatics 11-01-2012, 05:02 AM
Replies: 3
Views: 2,047
Posted By rndouglas
Tophat2: Not getting an accepted_hits.bam output

I am having some trouble with Tophat2/Bowtie2.

I ran the following:

tophat2 -p 4 -o ~/B73B2 -i 60 -I 4000 -G ~/gDNA.gtf ~/bowtie2_files/MaizeGDNA_B ~/B73B2.fastq


Everything seems to run...
Forum: Bioinformatics 10-29-2012, 03:22 PM
Replies: 0
Views: 1,202
Posted By rndouglas
Forum: Bioinformatics 08-27-2012, 03:10 PM
Replies: 2
Views: 1,586
Posted By rndouglas
Of course! Thank you! I'm guessing I just...

Of course! Thank you!

I'm guessing I just entered a bad sort command now.
Forum: Bioinformatics 08-27-2012, 01:46 PM
Replies: 2
Views: 1,586
Posted By rndouglas
SAM to BAM conversion issue

All of a sudden a problem with SAM to BAM conversion has cropped up for me.

I used Bowtie 1 to map sRNA reads to a sequence of interested and had a SAM file outputted:

@HD VN:1.0 SO:unsorted...
Forum: RNA Sequencing 08-27-2012, 03:56 AM
Replies: 3
Views: 1,373
Posted By rndouglas
Thanks for the suggestion! I also contacted...

Thanks for the suggestion!

I also contacted the program author directly and was told that this sort of thing has popped up with Illumina data before.

With Illumina input the program uses the...
Forum: RNA Sequencing 08-22-2012, 05:03 AM
Replies: 3
Views: 1,373
Posted By rndouglas
SeqTrimMap mapping issue

I have Illumina smallRNA-RNAseq reads that have already had their adapters removed and have been filtered for tRNA/rRNA.

I'm trying to use SeqTrimMap to align these reads to my reference genome...
Forum: Sample Prep / Library Generation 06-29-2012, 02:56 PM
Replies: 29
Views: 7,955
Posted By rndouglas
Talked to Epicentre today and learned that my...

Talked to Epicentre today and learned that my traces are exactly what I should expect to see. Wish I had just called them a couple months ago! Full speed ahead with library construction now...
Forum: Sample Prep / Library Generation 06-28-2012, 08:20 AM
Replies: 29
Views: 7,955
Posted By rndouglas
I only need 50 ng for my library prep, and I have...

I only need 50 ng for my library prep, and I have about 300 ng, so that's not an issue.

This was done on a pico chip.

Shouldn't I see a little bump for mRNA on the X-axis somewhere?

This is...
Forum: Sample Prep / Library Generation 06-27-2012, 12:51 PM
Replies: 29
Views: 7,955
Posted By rndouglas
Finally got my new Bioanalyzer results back, and...

Finally got my new Bioanalyzer results back, and I can't say I'm encouraged.

I used the Zymo kit to remove the big tRNA peak and wanted to see if I had any mRNA left.

Should I just trash these...
Forum: Sample Prep / Library Generation 06-15-2012, 06:21 AM
Replies: 29
Views: 7,955
Posted By rndouglas
I'm in the process of trying Phillip's suggesting...

I'm in the process of trying Phillip's suggesting right now. And by that I mean I'm still waiting for our DNA core to run the Bioanalyzer now that I've tried to remove all the smaller RNAs with the...
Forum: Sample Prep / Library Generation 06-01-2012, 05:42 PM
Replies: 29
Views: 7,955
Posted By rndouglas
RiboZero - Disappearing mRNA?

I'm having some trouble with Epicentre's RiboZero Plant Leaf Kit, and I'm hoping someone here might be able to point me in the right direction.

I have been isolating total RNA from maize leaves...
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