SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 20 of 20
Search took 0.00 seconds.
Search: Posts Made By: DFJ111
Forum: Bioinformatics 10-02-2012, 06:07 PM
Replies: 40
Views: 20,864
Posted By DFJ111
If the problem is occurring when using...

If the problem is occurring when using filter-stage-1.prl check that TRF and nseg are properly installed and on your PATH. I had the same problem but I can't actually remember how I solved it.. it's...
Forum: Bioinformatics 09-30-2012, 04:34 PM
Replies: 40
Views: 20,864
Posted By DFJ111
By the way Zimbobo, if you're doing de novo...

By the way Zimbobo, if you're doing de novo repeat element predictions you won't need existing repeat element libraries at all. You generate them yourself.
Forum: Bioinformatics 09-30-2012, 04:31 PM
Replies: 40
Views: 20,864
Posted By DFJ111
Here's an example of a run I did successfully. I...

Here's an example of a run I did successfully. I never got RepeatModeler working, and the installation of the standalone Blast program RMblast was a bit tricky. Make sure TRF and nseg are working...
Forum: Bioinformatics 09-27-2012, 02:40 PM
Replies: 2
Views: 1,956
Posted By DFJ111
Automating intron discovery in EST-derived gene models

So, yes, I have a large number of gene models that are derived from EST data. That is, the coding sequence is correct but any introns will be missing. I also have a bunch of 454 genomic sequence...
Forum: Bioinformatics 09-18-2012, 04:29 PM
Replies: 2
Views: 1,179
Posted By DFJ111
Thumbs up SNP calling vs. individual curated genes using 454 data from multiple heterozygotes

Hi.. yes, the title says it all. I need to identify novel SNPs (or, for that matter, any polymorphisms) in a bunch of curated genes (1500 or so). We don't have a genome. I have a lot of 454 exome...
Forum: Bioinformatics 09-10-2012, 06:01 PM
Replies: 14
Views: 6,269
Posted By DFJ111
^^ This worked for me. Thanks!

^^ This worked for me. Thanks!
Forum: Bioinformatics 08-29-2012, 03:09 PM
Replies: 3
Views: 1,176
Posted By DFJ111
Alternatively you could use Galaxy if you're not...

Alternatively you could use Galaxy if you're not keen on writing scripts. Galaxy works quite well with tab-delimited files.

Either way, I'm assuming the coordinates refer to a DNA sequence file...
Forum: Bioinformatics 08-27-2012, 05:02 PM
Replies: 3
Views: 1,995
Posted By DFJ111
I'm not sure it's a good idea, what are you doing...

I'm not sure it's a good idea, what are you doing in your pipeline? If your pipeline assumes that all sequences are the same length (as Illumina reads are) it might have issues with the variable read...
Forum: Bioinformatics 08-21-2012, 04:34 PM
Replies: 6
Views: 2,394
Posted By DFJ111
Personally I found CLC pretty but glitchy and too...

Personally I found CLC pretty but glitchy and too expensive. Unbelievably they had no facility to annotate with a .gff file except as a plugin. Did one lineup where an A and a C were considered to be...
Forum: Bioinformatics 08-20-2012, 07:53 PM
Replies: 5
Views: 1,291
Posted By DFJ111
Two reasons 1) You get more sequence 2) The...

Two reasons
1) You get more sequence
2) The two reads are separated by a region where you do not know the sequence, but you do know the distance between the reads. Genome assembly programs can use...
Forum: Bioinformatics 08-20-2012, 06:54 PM
Replies: 26
Views: 6,649
Posted By DFJ111
If by "power" you mean "memory", this thread...

If by "power" you mean "memory", this thread might be relevant:

http://seqanswers.com/forums/showthread.php?t=2101

Talks about memory requirement for velvet, which is pretty memory-hungry. So...
Forum: Bioinformatics 08-16-2012, 08:00 PM
Replies: 7
Views: 4,233
Posted By DFJ111
Not sure why you have duplicates of sample1 lane1...

Not sure why you have duplicates of sample1 lane1 read 1_002, sample1 lane2 read 1_002, and sample1 lane3 read 1_002. Typo from the sequencing lab? If all you want to do is QC (via FastQC for...
Forum: Bioinformatics 08-16-2012, 07:33 PM
Replies: 26
Views: 6,649
Posted By DFJ111
Gossamer: ...

Gossamer:

http://www.ncbi.nlm.nih.gov/pubmed/22611131

claims to be close to the theoretical lower limit for memory usage for de bruijn graph de novo assemblers.
Forum: Bioinformatics 08-15-2012, 03:25 PM
Replies: 6
Views: 3,826
Posted By DFJ111
63. Velvet doesn't like even numbered kmer values...

63. Velvet doesn't like even numbered kmer values (something to do with it not dealing well with palindromes). So you'd never use 64 as an actual kmer value.
Forum: Bioinformatics 08-13-2012, 04:41 PM
Replies: 1
Views: 893
Posted By DFJ111
Hi, I am dealing with similar problems.. I am...

Hi, I am dealing with similar problems.. I am reading through this special edition, which might be useful..

http://genomebiology.com/content/12/9

I know that some assemblers (e.g. MIRA3 with...
Forum: Bioinformatics 08-12-2012, 05:05 PM
Replies: 6
Views: 3,826
Posted By DFJ111
http://en.wikipedia.org/wiki/Integer_overflow ...

http://en.wikipedia.org/wiki/Integer_overflow

Is this relevant? Also, if you have to use a page file (i.e. hard drive) for extra memory, it will probably mean the assembly takes far too long...
Forum: Bioinformatics 08-12-2012, 01:57 PM
Replies: 9
Views: 3,012
Posted By DFJ111
Thanks. That's a paper on transcriptome data...

Thanks. That's a paper on transcriptome data though. Exome sequencing will be far less heterogeneous, although still heterogeneous enough that just throwing it into a normal genome assembly pipeline...
Forum: Bioinformatics 08-09-2012, 02:58 PM
Replies: 9
Views: 3,012
Posted By DFJ111
FYI In case anyone else encounters this, I have...

FYI In case anyone else encounters this, I have used MIRA3, which seems to have produced some good results. It has specific switches for heterogeneous coverage: using "est" in the -job switch (i.e....
Forum: Bioinformatics 08-08-2012, 02:09 PM
Replies: 9
Views: 3,012
Posted By DFJ111
Thanks.. yes, I'll try MIRA. The main reason I...

Thanks.. yes, I'll try MIRA. The main reason I used velvet is because 1) I'm familiar with it and 2) I'm familiar with how to preprocess fastq files based on quality/homopolymer runs, but not so much...
Forum: Bioinformatics 08-07-2012, 08:27 PM
Replies: 9
Views: 3,012
Posted By DFJ111
Wink De novo assembly of 454 exome sequencing

Hi people, just wanted some advice on a situation.

I have a dataset of 454 genome sequencing that has been enriched for gene-rich regions by using biotinylated RNA as a bait .. i.e. anything that...
Showing results 1 to 20 of 20

 


All times are GMT -8. The time now is 07:36 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO