SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA_seq on (non-model) less well annotated genomes Drerio General 5 06-10-2012 11:46 PM
non-matching barcodes PFS Bioinformatics 4 05-23-2011 12:57 PM
Sample quality for RNA_SEQ cub103 Sample Prep / Library Generation 3 08-02-2010 06:26 AM
cuffcompare not matching reference genome genec Bioinformatics 11 06-08-2010 09:35 AM
Low matching from capture libraries cmm8cmm8 SOLiD 3 11-27-2009 07:56 AM

Reply
 
Thread Tools
Old 11-24-2009, 01:35 PM   #1
sanush
Member
 
Location: san diego

Join Date: Nov 2009
Posts: 14
Default % matching problem- RNA_Seq

Hi
I am a new SOLiD user, and completed our first RNA-Seq experiment. I have a question regd the secondary analysis report. For the secondary analysis we uploaded whole human genome as reference and the % matched summary report for our 2 samples were around 25%. But according to ABI the run is considered successful only if the % match is above 30%. Can anyone comment on what the problem might be of low % match.

Thanks
sanush is offline   Reply With Quote
Old 11-29-2009, 09:58 PM   #2
lmf_bill
Member
 
Location: New Haven

Join Date: Jul 2008
Posts: 36
Default

Quote:
Originally Posted by sanush View Post
Hi
I am a new SOLiD user, and completed our first RNA-Seq experiment. I have a question regd the secondary analysis report. For the secondary analysis we uploaded whole human genome as reference and the % matched summary report for our 2 samples were around 25%. But according to ABI the run is considered successful only if the % match is above 30%. Can anyone comment on what the problem might be of low % match.

Thanks
The mapping percentage is correlated with the mismatches setting, the sequence length and the mapping procedure. You can allow more mismatches and mapping full-length and 1/3 trim-length. maybe, you can got higher percentage. you know, SOLiD generally has more mismatches than Solexa.
lmf_bill 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 05:41 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO