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Search: Posts Made By: Genomics101
Forum: General 05-26-2016, 02:05 PM
Replies: 1
Views: 1,924
Posted By Genomics101
Looking for a facility for optical mapping a non-model organism

Greetings.

I am looking for a facility, preferably in the US, that can work with us to make an optical map of a gastropod genome.

Nothing has been done like this before, but we have a lot of...
Forum: Bioinformatics 03-22-2016, 04:20 PM
Replies: 2
Views: 1,746
Posted By Genomics101
BUSCO runs to completion, but without gene predictions and no result. Help?

Greetings.

I would like to use BUSCO to get an idea of the level of completeness of the eukaryotic genomes I am working on. When I run BUSCO it goes to completion but finds no "BUSCOs." Looking...
Forum: Bioinformatics 02-03-2016, 07:36 AM
Replies: 0
Views: 1,111
Posted By Genomics101
Computational Karyotyping of non-model species genomes

Greetings.

I have some nice long read data for a diploid animal. There are no references species or even genera in this group and the karyotypes vary widely (from 12 to 50+ chromosomes).

Is...
Forum: Bioinformatics 09-17-2015, 10:22 AM
Replies: 2
Views: 1,645
Posted By Genomics101
Best error correction software and methods for de novo assembly of transcriptomes?

Greetings! It seems like a while (5 years) since this question was asked and I am sure there has been lots of progress on the topic in that time. I have a nice de novo assembly for a transcriptome...
Forum: Bioinformatics 08-26-2015, 04:36 AM
Replies: 1
Views: 2,670
Posted By Genomics101
Can't run GATK HaplotypeCaller set ploidy = 1

Greetings!

I have been attempting to call variants on a haploid genome using GATK HaplotypeCaller, however when I set ploidy = 1, I get an error:

INFO 21:05:57,644 HelpFormatter -...
Forum: Bioinformatics 08-21-2014, 12:04 PM
Replies: 2
Views: 1,733
Posted By Genomics101
Find out which adaptors/barcodes were used in an illumina library?

I have a bunch of Illimina MiSeq sequences that look like they might have some adaptor/barcode contamination. I'd like to do some adaptor trimming but need to know which set were used in the...
Forum: Bioinformatics 08-02-2014, 10:45 AM
Replies: 17
Views: 6,339
Posted By Genomics101
Thanks, Brian. This is where I am showing my...

Thanks, Brian. This is where I am showing my ignorance I am sure, but how did the reads become so short? Looking at what I pulled out of the sam file, they are full-length (300bp) reads for the...
Forum: Bioinformatics 08-02-2014, 10:21 AM
Replies: 17
Views: 6,339
Posted By Genomics101
Thanks very much, GenoMax. Indeed, it is MiSeq...

Thanks very much, GenoMax. Indeed, it is MiSeq data, but I never had this problem with MiSeq before (that was with 250bp PE reads, these are 300s). Can you tell me more the particular pathology...
Forum: Bioinformatics 08-02-2014, 08:52 AM
Replies: 17
Views: 6,339
Posted By Genomics101
A million thanks Brian, I have been puzzling over...

A million thanks Brian, I have been puzzling over this for days and with your help it was unraveled in just some hours. The key was looking for the reads with >2 placements, how did you know? Do you...
Forum: Bioinformatics 08-01-2014, 07:02 PM
Replies: 17
Views: 6,339
Posted By Genomics101
Removed all reads less that 200bp and quality...

Removed all reads less that 200bp and quality under 20 and viola:
http://i.imgur.com/LRdTYIg.png
Forum: Bioinformatics 08-01-2014, 06:17 PM
Replies: 17
Views: 6,339
Posted By Genomics101
Yes I am using BWA (MEM). Here is a read...

Yes I am using BWA (MEM).

Here is a read whose name shows up 8 times:

M01243:91:000000000-A6ELJ:1:2119:9911:4339 65 Pf3D7_14_v3 2584936 49 63M1D87M150S = 2584936 0 ...
Forum: Bioinformatics 08-01-2014, 05:44 PM
Replies: 17
Views: 6,339
Posted By Genomics101
Hi, Brian. I'm doing that now. In the mean...

Hi, Brian. I'm doing that now. In the mean time, here is how it looks with reads that only have unique positions: http://i.imgur.com/zNLG0ey.png

Although I didn't trim the reads I noticed that...
Forum: Bioinformatics 08-01-2014, 03:18 PM
Replies: 17
Views: 6,339
Posted By Genomics101
The mystery continues. I did all the analyses...

The mystery continues. I did all the analyses again with exactly the same results. Filtering for the primary alignments however gives me MORE reads in total than i have with just the original FASTQ...
Forum: Bioinformatics 08-01-2014, 01:20 PM
Replies: 17
Views: 6,339
Posted By Genomics101
This is true and and I puzzled by it as well. ...

This is true and and I puzzled by it as well. Although the number of reads went down after I extracted only the mapped reads (or so I thought), not enough. I'm going to make sure I am doing things...
Forum: Bioinformatics 08-01-2014, 12:42 PM
Replies: 17
Views: 6,339
Posted By Genomics101
Hi, Brian, thanks for your response. ...

Hi, Brian, thanks for your response.



This is not the case, the number or reads went from 1804074 total to 1801608 after filtering for unmapped reads. The maximum number on the Y-axis is...
Forum: Bioinformatics 08-01-2014, 11:56 AM
Replies: 17
Views: 6,339
Posted By Genomics101
Bizarre per sequence GC content distribution, what could cause this?

Greetings. I am working with an Illumina library of whole genome sequence for a very AT-rich genome. When I initially did a FASTQC I saw this: http://imgur.com/eVda7tD.png

The bimodal...
Forum: Bioinformatics 07-22-2014, 07:19 AM
Replies: 9
Views: 1,570
Posted By Genomics101
Best programs/methods for looking at mapped coverage? (Mapping whole genome data)

Greetings.

I'm interested in looking, in detail, at the mapped coverage for NGS short read data onto a reference, using whole genome data. I'd like a good way to examine and quantify the coverage...
Forum: Bioinformatics 04-25-2014, 07:49 AM
Replies: 4
Views: 2,764
Posted By Genomics101
@WhatsOEver Thanks! Here is an example of a...

@WhatsOEver

Thanks! Here is an example of a record for one CDS:

FT CDS 110938..112365
FT /colour=7
FT /ortholog="PFIT_0602100 PFIT_0602100;...
Forum: Bioinformatics 04-23-2014, 08:46 AM
Replies: 4
Views: 2,764
Posted By Genomics101
GO term enrichment with non-model organism (I have the GO terms for every locus)

Greetings. I am looking to do a GO-term enrichment analysis on a set of genes from an annotated genome whose GO terms are not loaded into the standard libraries. I have an EMBL formatted file with...
Forum: Bioinformatics 04-01-2014, 08:03 AM
Replies: 1
Views: 1,505
Posted By Genomics101
Problem extending/scaffolding contigs with MiSeq 250bp reads?

Greetings. I have some denovo assembled contigs (Velvet 1.2.10) made from 250bp MiSeq (Illumina) reads. After I make the contigs, I normally extend and scaffold them using SSPACE v1.0. This usually...
Forum: Bioinformatics 02-21-2014, 05:07 PM
Replies: 17
Views: 5,424
Posted By Genomics101
Yes, there is a reference that is pretty close,...

Yes, there is a reference that is pretty close, <2% difference at the base level, with a few rearrangements likely. I use Btrim for the trimming.
Forum: Bioinformatics 02-21-2014, 03:54 PM
Replies: 17
Views: 5,424
Posted By Genomics101
Thanks. I didn't trim by length, but by quality...

Thanks. I didn't trim by length, but by quality (Q30 cut off) and the reads just came out with most of them at around. But doing a less strict trimming may be the answer.

Since I have your very...
Forum: Bioinformatics 02-21-2014, 03:39 PM
Replies: 17
Views: 5,424
Posted By Genomics101
I also have the option of using the longer and...

I also have the option of using the longer and more uniform untrimmed reads, but the quality is pretty questionable:

http://i.imgur.com/bzNhrEm.png

I tried doing an assembly with these and got...
Forum: Bioinformatics 02-21-2014, 03:16 PM
Replies: 17
Views: 5,424
Posted By Genomics101
http://i.imgur.com/sRp7aKm.png

http://i.imgur.com/sRp7aKm.png
Forum: Bioinformatics 02-21-2014, 02:49 PM
Replies: 17
Views: 5,424
Posted By Genomics101
@AdrianP Thanks for your reply, but I actually...

@AdrianP Thanks for your reply, but I actually did kmers (with a larger gap between them ) all the way up to 191 as the initial analysis:
http://i.imgur.com/SBibmnL.png
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