Forum: Genomic Resequencing
09-23-2015, 01:42 PM
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Replies: 1
Views: 3,453
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Forum: Bioinformatics
10-24-2014, 08:52 AM
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Replies: 0
Views: 1,703
Trinity isoforms vs genes
Hi,
I am trying to assemble the transcriptome of a highly heterozygous species that may also be a tetraploid. I am using Trinity for that purpose, and was wondering how the program differentiates...
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Forum: Bioinformatics
06-20-2014, 06:52 AM
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Replies: 1
Views: 1,912
Solution?
It may be that this error is related to memory usage. Doubling the memory seems to have fixed the problem. Trinity ran all the way through to the end.
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Forum: Bioinformatics
06-19-2014, 02:28 PM
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Replies: 1
Views: 1,912
Trinity Chrysalis died with exit code 9
Hi, I'm running Trinity v 4.4.5 to perform some de novo assemblies using PE data. I get an error at the ReadsToTranscripts step, as follows:
followed by:
Does anyone know what exit code 9...
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Forum: Illumina/Solexa
05-27-2014, 10:46 AM
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Replies: 0
Views: 2,989
RAD-seq adapter design
Hi
I was planning a RAD-seq experiment for about 90 ecotypes. The costs of ordering 180+ HPLC purified and modified oligos for those many samples are quite prohibitive. Hence, I was thinking of a...
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Forum: De novo discovery
01-31-2014, 10:05 AM
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Replies: 1
Views: 2,209
Which assemblies are you trying to merge? I'm...
Which assemblies are you trying to merge? I'm confused because you say your best assembly is with 55 kmer. Why not just stick with that? That's what typically done.
FYI, on the page above it says...
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Forum: Illumina/Solexa
01-29-2014, 09:26 AM
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Replies: 2
Views: 2,881
Thanks for the quick reply, Dr. Johnson!
I...
Thanks for the quick reply, Dr. Johnson!
I am working with a tomato species, genome might be 900-1000Mb with 38% GC, based on what we know for cultivated tomato.
About coverage...my...
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Forum: Sample Prep / Library Generation
01-29-2014, 09:04 AM
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Replies: 5
Views: 2,862
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Forum: Sample Prep / Library Generation
01-29-2014, 08:15 AM
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Replies: 5
Views: 2,862
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Forum: De novo discovery
01-29-2014, 08:12 AM
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Replies: 2
Views: 2,050
Method for targeted sequencing
Hi,
My goal is to obtain the sequence of a gene from several species. I know the sequence only in 2 species separated by ~30mya. Designing optimal primers is not an option, since if the PCR...
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Forum: Sample Prep / Library Generation
01-29-2014, 08:03 AM
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Replies: 5
Views: 2,862
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Forum: Illumina/Solexa
01-29-2014, 07:27 AM
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Replies: 4
Views: 2,837
Is this RNA-seq or genomic sequencing? Can you...
Is this RNA-seq or genomic sequencing? Can you post a few more details about the expt? What are you going to do afterwards? Assembly?
From what you've posted above, the %AT/%GC looks too uniform...
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Forum: Illumina/Solexa
01-29-2014, 07:08 AM
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Replies: 2
Views: 2,881
Feedback on RAD-seq strategy
Hi,
I'm designing an experiment for RAD-seq and I was wondering if I could get some feedback about my experimental design.
I am looking to RAD-seq ~75 individuals of a highly heterozygous...
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Forum: Sample Prep / Library Generation
01-29-2014, 06:25 AM
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Replies: 0
Views: 2,882
Designing P1 P2 adapters for RAD-seq
Hi,
I am doing some research on how to design the optimal P1 and P2 adapters for RAD-seq, and had a couple of questions.
I know the P1 adapter consists of 5'-ForwardAmplificationPrimerSite...
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Forum: Bioinformatics
07-05-2013, 09:46 PM
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Replies: 0
Views: 1,797
edgeR: Common dispersion and pseudocounts
Common dispersion will tell me how much variability I should expect, on an average, in a given gene's mean expression value. Is that the variability due to technical effects or biological effects?
...
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Forum: Bioinformatics
03-13-2013, 08:22 AM
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Replies: 6
Views: 2,610
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Forum: Bioinformatics
11-05-2012, 04:41 PM
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Replies: 0
Views: 1,346
BFAST easyalign default
Hi,
I was wondering what the defaults for BFAST postprocess command for paired end SOLiD reads are? With the -p command, it gives
Does this mean it is flexible or that those are indeed the...
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Forum: Bioinformatics
10-23-2012, 09:32 AM
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Replies: 1
Views: 4,659
SOLiD csfasta to fastq using BFAST+BWA
Hi,
I'm trying to convert my SOLiD reads to FASTQ using BFAST+BWA's solid2fastq.pl utility. I have two sets of paired-end files
However, the solid2fastq.pl utility only allows files labeled...
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Forum: Bioinformatics
10-18-2012, 07:55 AM
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Replies: 132
Views: 54,827
Hi Marcel,
As I said above, cutadapt worked...
Hi Marcel,
As I said above, cutadapt worked well to trim the adapters. I used the following command line
cutadapt-1.1/bin/cutadapt --colorspace --trim-primer -e 0.12 -a 2130003001020221302222 -a...
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Forum: Bioinformatics
10-01-2012, 11:50 AM
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Replies: 6
Views: 2,610
Hi nilshomer,
Thanks for the reply. I'm...
Hi nilshomer,
Thanks for the reply. I'm making the index using the bfast fasta2brg function while specifying -A 1. The genome is in base space, however I want to align colorspace reads to it. Am I...
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Forum: Bioinformatics
09-26-2012, 12:57 PM
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Replies: 6
Views: 2,610
BFAST match error
Hi,
I'm getting the following error from BFAST with my colorspace SOLiD reads in FASTQ format. Couldn't figure out what it is...
All my reads are >20bp and I'm using a subset of all reads to...
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Forum: Bioinformatics
09-14-2012, 08:11 AM
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Replies: 132
Views: 54,827
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Forum: Bioinformatics
09-13-2012, 01:19 PM
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Replies: 132
Views: 54,827
cutadapt for solid reads
Hi,
I'm using cutadapt tool v1.1 to trim adapters from my SOLiD colorspace reads. The tool does trim the adapters out, however, I haven't been able to get my reads back in colorspace. cutadapt has...
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Forum: SOLiD
09-08-2012, 05:52 PM
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Replies: 5
Views: 5,029
A very basic script
I couldn't find any code for doing this, so wrote a quick python script. I've validated it using a couple of test sequences in the Data Formats file from ABI...
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Forum: Bioinformatics
04-20-2012, 12:57 PM
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Replies: 2
Views: 2,078
MUMmer's (probably) strange behavior
Hi,
I'm trying to use MUMmer to align two plant genomes - A. thaliana (120MB) and A. lyrata (240MB). The two species are fairly close - 5 million years - similar to humans and chimps.
I used...
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