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Forum: Bioinformatics 05-04-2012, 03:57 AM
Replies: 7
Views: 3,013
Posted By cerebralrust
Hello members. Thank you for your valuable...

Hello members. Thank you for your valuable advice.

I've run assemblies on my data using Trinity,Newbler,MIRA,velvet on my HP laptop which has 4GB RAM and i3 processsor. About 800k reads with both...
Forum: Bioinformatics 04-29-2012, 12:53 AM
Replies: 7
Views: 3,013
Posted By cerebralrust
Exclamation Differential gene expression analysis without reference

I have to find the differential gene expression between two genotypes of a plant species sequenced using 454 pyrosequencer.

There is no reference genome and the closest species -glycine max aligns...
Forum: 454 Pyrosequencing 04-27-2012, 07:48 AM
Replies: 0
Views: 1,751
Posted By cerebralrust
Exclamation 1/4th of microtitre plate enough to characterize transcriptome of non-model legume?

Dear Members,

In your experience, do you think 1/4th of a microtitre plate is enough to characterize the genome of a non-model legume species?

The 454 sequencing performed in the above fashion...
Forum: Bioinformatics 02-25-2012, 01:27 AM
Replies: 8
Views: 4,200
Posted By cerebralrust
Thank you for all your suggestions, members! ...

Thank you for all your suggestions, members!

@ seqret : As Rick pointed out, i've never used Newbler.

@ Rick : Using Newbler is not an option, i guess, since it is not open source and we got...
Forum: Bioinformatics 02-23-2012, 07:05 AM
Replies: 8
Views: 4,200
Posted By cerebralrust
Exclamation Too few reads mapping back to contigs

I assembled plant transcriptome 454 data (non normalised) using trinity after the following

1)pre processing (removal of adaptors, vector contamination)
2)removal of rRna sequences
3)removal of...
Forum: Bioinformatics 02-10-2012, 09:09 AM
Replies: 4
Views: 2,939
Posted By cerebralrust
Thank you very much for your reply, Rick! ...

Thank you very much for your reply, Rick!

I'm using both MIRA and Trinity for assembly. Trinity is supposedly less sensitive to low quality compared to MIRA.

Anyhow, i will stick to removal of...
Forum: Bioinformatics 02-10-2012, 07:32 AM
Replies: 4
Views: 2,939
Posted By cerebralrust
Exclamation Extent of reduction during pre-processing

I'm just curious as how much reduction others observe during pre-processing of ngs data.

I've got 454 rna-seq data of about 300,000 reads.
Based on the fastqc report and using fastx toolkit,
-...
Forum: RNA Sequencing 01-30-2012, 09:45 PM
Replies: 0
Views: 1,599
Posted By cerebralrust
Exclamation Repetitiveness of genome and assembly

Hello.
We've got Rna-seq data from sequencing a legume crop. There is no reference genome nor EST data available.
We assembled the data using MIRA including the highly repetitive option, since it...
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