Forum: Bioinformatics
05-04-2012, 03:57 AM
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Replies: 7
Views: 2,981
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...
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Forum: Bioinformatics
04-29-2012, 12:53 AM
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Replies: 7
Views: 2,981
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Forum: 454 Pyrosequencing
04-27-2012, 07:48 AM
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Replies: 0
Views: 1,729
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Forum: Bioinformatics
02-25-2012, 01:27 AM
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Replies: 8
Views: 4,155
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...
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Forum: Bioinformatics
02-23-2012, 07:05 AM
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Replies: 8
Views: 4,155
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...
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Forum: Bioinformatics
02-10-2012, 09:09 AM
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Replies: 4
Views: 2,863
Thank you very much for your reply, Rick!
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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...
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Forum: Bioinformatics
02-10-2012, 07:32 AM
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Replies: 4
Views: 2,863
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,
-...
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Forum: RNA Sequencing
01-30-2012, 09:45 PM
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Replies: 0
Views: 1,578
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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