Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
454 - Transcriptome SNPs Detection Giorgio C Bioinformatics 3 02-12-2013 12:21 AM
Starting cancer transcriptome analysis of 454 sequencing data ketan_bnf Bioinformatics 1 09-11-2011 11:35 PM
not enough isogroups in 454 transcriptome? litali Bioinformatics 6 01-25-2011 06:41 PM
De-Novo transcriptome with 454 Titanium yvan.wenger RNA Sequencing 3 10-29-2009 12:19 AM

Thread Tools
Old 02-03-2011, 09:12 AM   #1
Location: Netherlands

Join Date: Dec 2009
Posts: 13
Default 454 transcriptome analysis


I have a question regarding the 454 transcriptome (cdna) analysis.

Would it be correct to assume that a 454AllContigs.fna in newbler cDNA assembly directory is a non-redundant version of -all- the reference bases that are in the 454Isotigs.fna file?

I would like to carry out a read mapping on a set where there are no exons in multiple isotigs but is represented only once (in contigs) so that the mapping quality is kept high when using bwa bwasw.

Thanks for answers.
CHRYSES is offline   Reply With Quote
Old 02-07-2011, 04:56 AM   #2
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415

That would have been nice, now, wouldn't it.... Unfortunately, depending on your sample, you might find very similar contigs with just a few base changes between them. Small sequence variations can cause this behavior. Perhaps in the ideal case of all samples coming from the same organism that in addition is homozygous on all loci (e.g. haploid or double haploid) would you find unique contigs only.

To make a non-redundant contig dataset would require clustering (using CD-HIT or other tools), within isogroups perhaps.
flxlex is offline   Reply With Quote

454, cdna, contig, isotig, newbler

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 04:04 AM.

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