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Forum: RNA Sequencing 12-20-2011, 12:40 PM
Replies: 4
Views: 2,732
Posted By jmartin127
Precompiled executables have worked great for us...

Precompiled executables have worked great for us on Linux 64-bit Debian 5 machines.
Forum: Bioinformatics 08-12-2011, 09:44 PM
Replies: 5
Views: 5,717
Posted By jmartin127
We usually use Blat for this type of thing. It...

We usually use Blat for this type of thing. It does a fairly good job.
Forum: RNA Sequencing 06-13-2011, 06:36 AM
Replies: 7
Views: 3,459
Posted By jmartin127
Often when I've done this type of analysis, I've...

Often when I've done this type of analysis, I've aligned my reads to the spliced transcript sequences. For most organisms this will be listed as the "XXX_cDNA.fasta", for example. To get the...
Forum: RNA Sequencing 06-10-2011, 06:38 AM
Replies: 7
Views: 3,459
Posted By jmartin127
I see what you mean, I cannot say for sure why...

I see what you mean, I cannot say for sure why the values are so different from the two software programs. Are you aligning to the genome or to the transcripts themselves to calculate RPKM? Usually I...
Forum: RNA Sequencing 06-09-2011, 09:40 PM
Replies: 7
Views: 3,459
Posted By jmartin127
Since the reads you get from 454 will be DNA (the...

Since the reads you get from 454 will be DNA (the cDNA is sequenced), then you should align to a DNA reference. With 454 you may not have enough sequencing depth to get good RPKM measurements from a...
Forum: Bioinformatics 06-03-2011, 07:31 AM
Replies: 16
Views: 6,553
Posted By jmartin127
Thanks Cole for the quick fix. Version 1.3.0 is...

Thanks Cole for the quick fix. Version 1.3.0 is running successfully now.
Forum: RNA Sequencing 06-02-2011, 07:42 PM
Replies: 7
Views: 5,299
Posted By jmartin127
Aligning your de novo assembled transcriptome to...

Aligning your de novo assembled transcriptome to a genomic reference can help to determine which assembly is better. Presumably, whatever you are sequencing is a closely related plant to arabidopsis?...
Forum: RNA Sequencing 06-02-2011, 07:31 PM
Replies: 2
Views: 2,357
Posted By jmartin127
Welcome to RNA-Seq. You may want to first forget...

Welcome to RNA-Seq. You may want to first forget everything you learned about genome sequencing. :D

I would align the reads to the transcriptome FASTA file, assuming you have one, and check which...
Forum: RNA Sequencing 06-02-2011, 07:09 PM
Replies: 1
Views: 2,851
Posted By jmartin127
This has been fixed. But there is still another...

This has been fixed. But there is still another error. See:
http://seqanswers.com/forums/showthread.php?t=11793
Forum: Bioinformatics 06-02-2011, 07:07 PM
Replies: 16
Views: 6,553
Posted By jmartin127
Yep, same for me.

Yep, same for me.
Forum: Bioinformatics 04-23-2011, 08:18 PM
Replies: 1
Views: 3,926
Posted By jmartin127
Hi, I have been able to load RepeatMasker GFF...

Hi, I have been able to load RepeatMasker GFF files into IGV with no problem.

First off, I'm assuming you're using rmOutToGFF3.pl to convert the RepeatMasker output into GFF format, correct?...
Forum: De novo discovery 04-06-2011, 08:19 PM
Replies: 82
Views: 51,063
Posted By jmartin127
We've tried a few different programs for de novo...

We've tried a few different programs for de novo transcriptome assembly, you can see our paper that came out about a year ago here: http://www.biomedcentral.com/1471-2164/11/663.

As Marcel pointed...
Forum: Illumina/Solexa 01-05-2011, 01:37 PM
Replies: 6
Views: 8,474
Posted By jmartin127
FredOnSeq, would you mind pointing me to where...

FredOnSeq, would you mind pointing me to where you found the "stitch" software? I can't seem to find it by Google'ing. Thanks in advance.
Forum: Illumina/Solexa 07-08-2010, 10:23 AM
Replies: 2
Views: 1,580
Posted By jmartin127
This may help to clarify things for you:...

This may help to clarify things for you: http://en.wikipedia.org/wiki/FASTQ_format.
Forum: Bioinformatics 03-06-2010, 01:28 PM
Replies: 1
Views: 1,991
Posted By jmartin127
Did you check to make sure that BLAST is aligning...

Did you check to make sure that BLAST is aligning the full length of the contig?
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