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Forum: Genomic Resequencing 09-23-2015, 01:42 PM
Replies: 1
Views: 3,406
Posted By flobpf
Did you figure out a solution? I'm running into...

Did you figure out a solution? I'm running into the same problem 3 years later.
Forum: Bioinformatics 10-24-2014, 08:52 AM
Replies: 0
Views: 1,679
Posted By flobpf
Post 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...
Forum: Bioinformatics 06-20-2014, 06:52 AM
Replies: 1
Views: 1,900
Posted By flobpf
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.
Forum: Bioinformatics 06-19-2014, 02:28 PM
Replies: 1
Views: 1,900
Posted By flobpf
Post 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...
Forum: Illumina/Solexa 05-27-2014, 10:46 AM
Replies: 0
Views: 2,952
Posted By flobpf
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...
Forum: De novo discovery 01-31-2014, 10:05 AM
Replies: 1
Views: 2,189
Posted By flobpf
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...
Forum: Illumina/Solexa 01-29-2014, 09:26 AM
Replies: 2
Views: 2,854
Posted By flobpf
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...
Forum: Sample Prep / Library Generation 01-29-2014, 09:04 AM
Replies: 5
Views: 2,845
Posted By flobpf
or RNA fragmentation due to incomplete...

or RNA fragmentation due to incomplete inactivation of RNAse from sample.
Forum: Sample Prep / Library Generation 01-29-2014, 08:15 AM
Replies: 5
Views: 2,845
Posted By flobpf
If that was the case, I think you'd see lighter...

If that was the case, I think you'd see lighter bands and lower RNA yields. You wouldn't see new bands.
Forum: De novo discovery 01-29-2014, 08:12 AM
Replies: 2
Views: 2,035
Posted By flobpf
Post 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...
Forum: Sample Prep / Library Generation 01-29-2014, 08:03 AM
Replies: 5
Views: 2,845
Posted By flobpf
Looks like RNA fragmentation or DNA contamination...

Looks like RNA fragmentation or DNA contamination to me. The peaks are well correlated with the gel. If it was the chip, you'd have seen it across all samples. You might want to run an agarose gel...
Forum: Illumina/Solexa 01-29-2014, 07:27 AM
Replies: 4
Views: 2,812
Posted By flobpf
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...
Forum: Illumina/Solexa 01-29-2014, 07:08 AM
Replies: 2
Views: 2,854
Posted By flobpf
Post 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...
Forum: Sample Prep / Library Generation 01-29-2014, 06:25 AM
Replies: 0
Views: 2,848
Posted By flobpf
Post 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...
Forum: Bioinformatics 07-05-2013, 09:46 PM
Replies: 0
Views: 1,783
Posted By flobpf
Exclamation 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?
...
Forum: Bioinformatics 03-13-2013, 08:22 AM
Replies: 6
Views: 2,572
Posted By flobpf
I don't recollect how my problem got solved, but...

I don't recollect how my problem got solved, but probably the solution was changing the version of BFAST. My other glibc problems have certainly been solved by changing the version of the program in...
Forum: Bioinformatics 11-05-2012, 04:41 PM
Replies: 0
Views: 1,335
Posted By flobpf
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...
Forum: Bioinformatics 10-23-2012, 09:32 AM
Replies: 1
Views: 4,624
Posted By flobpf
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...
Forum: Bioinformatics 10-18-2012, 07:55 AM
Replies: 132
Views: 54,518
Posted By flobpf
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...
Forum: Bioinformatics 10-01-2012, 11:50 AM
Replies: 6
Views: 2,572
Posted By flobpf
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...
Forum: Bioinformatics 09-26-2012, 12:57 PM
Replies: 6
Views: 2,572
Posted By flobpf
Question 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...
Forum: Bioinformatics 09-14-2012, 08:11 AM
Replies: 132
Views: 54,518
Posted By flobpf
That helps. Thanks OK. Thats better. I...

That helps. Thanks


OK. Thats better. I had misunderstood what double-encoding is.

Thanks for your help!
Forum: Bioinformatics 09-13-2012, 01:19 PM
Replies: 132
Views: 54,518
Posted By flobpf
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...
Forum: SOLiD 09-08-2012, 05:52 PM
Replies: 5
Views: 5,003
Posted By flobpf
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...
Forum: Bioinformatics 04-20-2012, 12:57 PM
Replies: 2
Views: 2,060
Posted By flobpf
Post 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...
Showing results 1 to 25 of 76

 


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