SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
MIRA3 multiple input files from same tech grassgirl Bioinformatics 6 11-10-2011 09:09 AM
SRA files for use in MIRA3 assembler seenstevo Bioinformatics 7 10-27-2011 05:14 AM
HTSeq output not correlated with Cufflinks output... Help gen2prot Bioinformatics 5 01-31-2011 09:16 AM
MIRA3: setup BAMBUS Configuration File problem facing edge Bioinformatics 0 10-01-2009 01:43 AM
MIRA3: Create Scaffold Fasta files problem edge Bioinformatics 0 09-30-2009 08:21 PM

Reply
 
Thread Tools
Old 01-27-2010, 01:43 AM   #1
damiankao
Member
 
Location: UK

Join Date: Jan 2010
Posts: 49
Default mira3 output

Hi I am a first year phd student trying my hand at bioinformatcs. I assembled about 190,000 454 reads with mira3 and I need some help going through the output.

The assembly info file indicated that I have 21,769 contigs. But the result fasta file shows around 24,000 sequences. I am assuming that the fasta sequences with the header name ending in 'c' (for example, >myProject_c1203) indicates a contig that was assembed. What are sequences that have header names ending in 's' or 'lrc' (>myproject_lrc2938).

Does mira3 discard sequences that it thinks is of low quality or too short? I noticed that the number of reads assembled is 119,794 (2508 singlets), whereas the number of reads I fed into mira3 was around 190,000.
damiankao is offline   Reply With Quote
Old 02-05-2010, 02:29 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

I think "c" means a contig, "s" means singleton, and "lrc" is also a contig but where there were problems with repeats. Try Google:
http://www.freelists.org/post/mira_t...file-and-lrc,1
maubp is offline   Reply With Quote
Old 02-05-2010, 07:10 AM   #3
AppleInformatics
Junior Member
 
Location: WNY

Join Date: Nov 2009
Posts: 5
Default

Hi Damiankao! I would stronlgy recommend signing up for the mira_talk mailing list (mira_talk@freelists.org) as well. The community is very friendly and Mira's author, Bastien Chevreux, answers questions everyday.
AppleInformatics is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:36 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO