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Old 02-25-2012, 12:27 AM   #7
cerebralrust
Junior Member
 
Location: Sweden

Join Date: Jan 2012
Posts: 8
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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 the sequenced data from a collaborator in the US. Perhaps my only option is to standardise mira parameters to improve the assembly?

@kmcarr : I was wondering about the mapping also. I will try mapping with bwasw and bowtie2 on the suggestion of lh3 since i require results in sam format also.

@lh3 : I will try all, compare and pick the best one.

@Jeremy : As i mentioned before, Newbler is not an option since it is not open source and i'm a poor undergraduate student. But i will keep your suggestions in mind for the future.

I suppose i'm left with the option of using mira with various combinations of parameters to get the best assembly.

If it may be of help to anyone, I should not have used Trinity for this data considering :

According to one of key developers of Trinity - Brian J. Haas' option:

"Ultimately, Trinity might not be the best tool for assembling 454 data, since coverage won't be anywhere near what is expected from Illumina in most cases, and Trinity exploits the high coverage data as part of reconstructing transcripts. The current version of Newbler is supposed to work especially well for 454 transcriptome data, so I encourage you to give that a try if you haven't already."
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