SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
bowtie reference genome index: help required kevlim83 Bioinformatics 11 12-09-2014 06:36 PM
Create vcf tribble index? brofallon Bioinformatics 2 07-13-2014 01:53 AM
looking to create IUPAC reference genome amythecat Bioinformatics 1 06-12-2013 11:42 PM
Create new Reference by merging SNV list with reference genome rdoan Bioinformatics 0 10-12-2012 07:17 AM
Assisted de novo genome assembly? Create new consensus mapping reads to reference? zmartine Bioinformatics 8 02-10-2012 12:31 AM

Reply
 
Thread Tools
Old 11-01-2013, 06:27 AM   #1
wmseq
Member
 
Location: IL

Join Date: May 2011
Posts: 71
Default Do I need to create an index for my reference genome?

Hi every one,
After I aligned the reads of my samples with tophat, do I need to to create an index for my reference genome like after bowtie2 alignment, and then convert/sort/index all my sam files to identify the upregulated and down-regulated genes from a compound treatment?
Thanks a lot!!
Richard
wmseq is offline   Reply With Quote
Old 11-01-2013, 07:45 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

No, you don't need to do that.
dpryan is offline   Reply With Quote
Old 11-01-2013, 08:09 AM   #3
wmseq
Member
 
Location: IL

Join Date: May 2011
Posts: 71
Default

Thank you, dpryan!!
Do I need to convert/sort/index all my sam files, because I saw a question on a problem with unsorted bam files for HTSeq-count?
wmseq is offline   Reply With Quote
Old 11-01-2013, 08:20 AM   #4
dariober
Senior Member
 
Location: Cambridge, UK

Join Date: May 2010
Posts: 311
Default

Quote:
Originally Posted by wmseq View Post
Thank you, dpryan!!
Do I need to convert/sort/index all my sam files, because I saw a question on a problem with unsorted bam files for HTSeq-count?
From my memory I recall tophat produces bam files sorted by position. htseq-count needs sam files sorted by read name only if the reads are paired-end. If they are single end I don't think the order matters.
dariober is offline   Reply With Quote
Old 11-01-2013, 08:29 AM   #5
wmseq
Member
 
Location: IL

Join Date: May 2011
Posts: 71
Default

But I read a tutorial, it seams that all sam files should be convert/sort/indexed. I am not sure.
wmseq is offline   Reply With Quote
Old 11-02-2013, 01:42 AM   #6
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

If you have paired end reads, then you need to name sort the file (usually you would sort a BAM file, rather than a SAM file). There's no need to create an index when using htseq-count, it will ignore it.
dpryan 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 12:29 AM.


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