Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa

Similar Threads
Thread Thread Starter Forum Replies Last Post
short reads mapping software with GUI needed asheenlevrai General 27 03-26-2012 01:44 PM
Mapping very short (<20 bp) reads hclee Bioinformatics 4 07-15-2011 08:53 AM
De novo fragment assembly with short mate-paired reads, Does the read length matter? strob Literature Watch 3 10-23-2009 01:36 PM
Uniquely mapped short reads (MAQ) bioinfosm Bioinformatics 8 03-30-2009 11:05 AM
MAQ and short read length (DGE) jms1223 Illumina/Solexa 5 02-23-2009 07:07 AM

Thread Tools
Old 12-30-2010, 07:57 PM   #1
Junior Member
Location: india

Join Date: Jul 2010
Posts: 1
Default Mapping Short Reads with unequal length using MAQ

hi everyone,

I m in the process of finding SNPs in miRNA sequence for which i have used known miRNA sequences as the reference and short reads of RNA sequence are mapped to it using MAQ.
The reads i m using is trimmed sequence so i dont supply the adapter sequence in the alignment option for MAQ.
The problem i m facing is in the alignment generated most of the reads are trimmed off automatically from the 3' end reducing it to 17 bp reads(original varies from 20,24,25). Some reads maintained thier original lenght in the alignment. And there is no obvious rule as to how the reads are trimmed(the trimmed length is not equal,).
Can anyone help me out?

Thanks in advance.
TOLEN is offline   Reply With Quote

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 11:07 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO