Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
snp call in Repeat Masked region caswater Bioinformatics 0 05-07-2012 08:10 PM
Zorro: The Masked Assembler (first public release) glacerda Bioinformatics 3 04-16-2011 05:11 AM
bwa masked sequence? rand Bioinformatics 2 11-09-2009 06:02 AM
why consed finds discrepancies with masked n sequence alig Illumina/Solexa 3 06-12-2009 12:32 PM
Masked/Unmasked Reference Genome ytmnd85 General 5 05-31-2009 03:52 PM

Thread Tools
Old 07-18-2012, 06:21 PM   #1
Junior Member
Location: Montevideo, Uruguay

Join Date: May 2012
Posts: 1
Default Un/Masked reads or reference genes

Hi All

I am kind of new in bioinformatic so i hope you cold help me!
Recently i made a microdissection LASER and i cut the long arm of chromosome Z from a cell line, then i amplified the DNA and obtain the sequence from illumina hi seq. The files contain 9 gb the lenght of the reads are 100pb paired end and 30X (coverage)
I need to identify the genes present in this chromosome arms but this cell line is newly sequence so i have the 24000 predicted genes as reference.
I used CLC genomic Workbench to made the alignment with the reads and the predicted genes. The result was that are some reference genes that present an a amount of reads higher in comparison with other reference genes. The only think i now from my sample is that contain a lot of repeats, so i think is thats the problem.
Any suggestion about masking the reference or the reads?
please i hope somebody help me!
losts of thanks

ire 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 04:15 PM.

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