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Forum: Bioinformatics 07-09-2014, 09:02 AM
Replies: 2
Views: 904
Posted By RNAddict
Extracting coding sequences from genomic scaffolds

I have a list of sequences (cDNA) that I want to find in many different organisms. I have obtained genomic scaffolds for these organisms from various locations.

I BLAST my cDNA sequences against...
Forum: De novo discovery 06-10-2014, 12:07 PM
Replies: 5
Views: 13,631
Posted By RNAddict
Brian - thanks for your insightful response. I'll...

Brian - thanks for your insightful response. I'll go ahead and try generating a kmer plot.

Your comment brings up a point that I am still a bit stuck on - that being what to call "duplicate." I...
Forum: De novo discovery 06-09-2014, 04:17 PM
Replies: 5
Views: 13,631
Posted By RNAddict
Brian, I appreciate your input. We have now...

Brian,
I appreciate your input. We have now gone through a few rounds of sequencing and assembly - our latest assembly is using Illumina 'longreads' >1500kb in addition to a number of SIMP PE...
Forum: De novo discovery 06-09-2014, 01:14 PM
Replies: 5
Views: 13,631
Posted By RNAddict
Gene duplication events vs. duplicate scaffolds

Hi all,
Recently I've been looking at a draft genome assembly a collaborator has sent me. The first thing I notice is that the size of the assembly is really big 3-4X the size of the estimated...
Forum: Bioinformatics 04-04-2013, 04:53 AM
Replies: 1
Views: 839
Posted By RNAddict
Bowtie input question - combining left and right reads?

Hi all,
I have some 100bp PE reads. I combined my left.fa and right.fa files into one file 'both.fa' and tried aligning these reads to my reference using Tophat/Bowtie.

Alignment ran to...
Forum: RNA Sequencing 03-29-2013, 04:42 AM
Replies: 9
Views: 3,375
Posted By RNAddict
Did you ever find a way to fix this second error?...

Did you ever find a way to fix this second error? I am experiencing it as well.
Forum: RNA Sequencing 03-27-2013, 11:27 AM
Replies: 9
Views: 3,375
Posted By RNAddict
Ramma could you supply me with your 8MB...

Ramma could you supply me with your 8MB compilation?
Forum: Bioinformatics 08-21-2012, 06:40 AM
Replies: 8
Views: 2,533
Posted By RNAddict
@SES: HMMER doesn't support nucleotide searches...

@SES: HMMER doesn't support nucleotide searches (similar to BLASTx) though right? I just have transcripts at this point. Given that, do you still think it would be best to use HMMER? E.g. identify...
Forum: Bioinformatics 08-17-2012, 11:37 AM
Replies: 8
Views: 2,533
Posted By RNAddict
Thanks for your responses. @SES: I am...

Thanks for your responses.

@SES: I am working with a fern, so not very related to Arabidopsis. But obviously more so then to Humans, Mouse, ect.

My protocol was going to be as follows:
1....
Forum: Bioinformatics 08-16-2012, 07:46 AM
Replies: 8
Views: 2,533
Posted By RNAddict
Which organism has the best GO annotations?

I was wondering if anyone had any thoughts on this topic. Basically I want to use GOrilla to find enriched GO terms between two samples. GOrilla requires that you use genes from 1 of 8 model...
Forum: De novo discovery 08-13-2012, 11:01 AM
Replies: 0
Views: 1,236
Posted By RNAddict
Mapping to subsets of a transcriptome reference?

I have made 'reference' transcriptomes from several different isolates. I have tried mapping my RNAseq reads with the tuxedo suite to these transcriptomes in order to conduct DE. Some transcripts...
Forum: Bioinformatics 05-23-2012, 09:57 AM
Replies: 2
Views: 1,606
Posted By RNAddict
Below is an example from my accepted_hits.bam...

Below is an example from my accepted_hits.bam file I am trying to run with cufflinks
...
Forum: Bioinformatics 05-23-2012, 08:52 AM
Replies: 2
Views: 1,606
Posted By RNAddict
Cufflinks problem sorting

I have mapped reads to a reference using tophat/bowtie. I then use the output from tophat with cufflinks... and I get the following error "sort order of reads in BAMs must be the same."

I have...
Forum: Bioinformatics 04-10-2012, 05:19 AM
Replies: 0
Views: 1,487
Posted By RNAddict
Trinity probpath missing from successful butterfly runs

My issue: I run trinity and 1 butterfly job fails. I rerun butterfly for the failed job and it successfully finishes. I go to concatenate all my successful jobs

find trinity_out_dir/chrysalis...
Forum: Bioinformatics 04-03-2012, 11:54 AM
Replies: 12
Views: 3,808
Posted By RNAddict
We are having a similar experience. We de novo...

We are having a similar experience. We de novo assembled a transcriptome we are using as a "reference" but when we map reads to that we get so many multi-mapped reads that many transcripts that we...
Forum: Bioinformatics 03-30-2012, 01:43 PM
Replies: 2
Views: 1,361
Posted By RNAddict
Comparing mapped reads

I have used Tophat to map reads to a reference sequences. I would like to identify reads that mapped to multiple sequences. Does anyone know how this can be accomplished?

E.g. I would like to be...
Forum: General 03-16-2012, 11:18 AM
Replies: 2
Views: 1,146
Posted By RNAddict
Using NGS sequences before publishing

I don't know if this has been encountered before (although it seems very likely) but I am wondering about the conventions or feelings people and editors have about using sequences generated from NGS...
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