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Forum: Open Genomics Engine Project 04-30-2013, 07:36 AM
Replies: 14
Views: 43,780
Posted By BobFreemanMA
Sounds great. Thanks!

Sounds great. Thanks!
Forum: Open Genomics Engine Project 04-29-2013, 07:22 AM
Replies: 14
Views: 43,780
Posted By BobFreemanMA
And this is different from Galaxy in what ways???

This seems very exciting and promising, but I hope that you can tell me how this project is different from Galaxy. And it seems to have a significant advantage in terms of release time, users,...
Forum: Bioinformatics 02-05-2013, 05:39 AM
Replies: 3
Views: 2,391
Posted By BobFreemanMA
Not sure what the spec says. I tried to...

Not sure what the spec says. I tried to concatenate the two files and use that, but the program I submitted the concatenated file to barfed with the error 'duplicate gene id' (or something like...
Forum: Bioinformatics 02-04-2013, 03:51 PM
Replies: 3
Views: 2,391
Posted By BobFreemanMA
Merge two gff3 files?

I have two gff3 files, one of primary transcripts and one of alternative transcripts, that need to be merged into one file. Since the files must be interwoven (some gene IDs appear in both), simply...
Forum: Bioinformatics 02-01-2013, 07:39 AM
Replies: 2
Views: 1,349
Posted By BobFreemanMA
In theory, this is true. However, RNA-seq is so...

In theory, this is true. However, RNA-seq is so sensitive that it is likely one is also capturing pre-spliced and partially spliced mRNAs, although in very low %s. These species of molecules are the...
Forum: Bioinformatics 11-30-2012, 05:52 AM
Replies: 16
Views: 8,362
Posted By BobFreemanMA
Check out the gffread utility as a part of...

Check out the gffread utility as a part of cufflinks programs. One of the options allows you to read from GFF3 and convert to GTF. See the info at http://cufflinks.cbcb.umd.edu/gff.html

-Bob
Forum: Bioinformatics 11-16-2012, 09:26 AM
Replies: 2
Views: 1,349
Posted By BobFreemanMA
Identifying intron sequences in de novo assembled transcripts?

Greetings!

We're using Trinity to do de novo assembly of frog RNA-seq data. From the resulting assemblies, I'd like to be able to identify any transcripts that contain intronic sequences (from...
Forum: Bioinformatics 11-21-2011, 08:10 AM
Replies: 1
Views: 2,001
Posted By BobFreemanMA
Mapping paired reads to de novo RNA-seq assemblies for quality assessment?

Greetings!

I'm working with paired end reads (not strand-specific; 100 bp each end with a total fragment size of 400 bp) from Illumina v1.5 data format; 100 million read pairs, but trying out the...
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