SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Single end read with paired end reads tahamasoodi Bioinformatics 2 01-16-2016 08:46 AM
assemble single-read and paired-end read morning latte Bioinformatics 5 08-28-2013 12:09 PM
Removing short reads from paired-end fastqs jakeenk Bioinformatics 0 07-11-2013 09:00 AM
RNA-seq: read counts in single- vs paired-end sequences fbarreto Illumina/Solexa 4 08-03-2011 06:19 PM
Difference in paired-end and single-end read ? darshan Bioinformatics 1 10-01-2009 12:44 AM

Reply
 
Thread Tools
Old 12-30-2013, 05:29 PM   #1
Genomics101
Member
 
Location: Maryland, USA

Join Date: May 2012
Posts: 60
Default Velvet 1.2.10 with FASTQs of different read-lengths AND paired- and single-end?

Greetings.

I have been using Velvet 1.2.10 to create de novo assembled contigs with good results using 100bp paired-end reads.

Now I have more and different data, because I have longer reads and because I now trim for quality using Btrim64. As a result, from the two original sets of paired-end reads, 100 and 250bp reads (with 400 and 600 bp insert sizes, respective) I have 4 sets of reads:

Sample1_100bp_R1.fastq.pe
Sample1_100bp_R2.fastq.pe
Sample1_100bp_R1.fastq.se
Sample1_100bp_R2.fastq.se
Sample1_250bp_R1.fastq.pe
Sample1_250bp_R1.fastq.pe
Sample1_250bp_R2.fastq.pe
Sample1_250bp_R1.fastq.se
Sample1_250bp_R2.fastq.se

(The single reads result when the pair is sacrificed in the quality trimming)

I have 3 questions:

Is it possible to combine all of these data for a de novo assembly in Velvet?

Are the 250bp reads still considered short reads or are they long reads?

Is there a problem now that the read-length is no longer consistent due to trimming?

Thanks!
Genomics101 is offline   Reply With Quote
Old 12-31-2013, 03:53 AM   #2
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 662
Default

Quote:
Originally Posted by Genomics101 View Post

Is it possible to combine all of these data for a de novo assembly in Velvet?
Yes. You may have to recompile velvet to run with a larger number of categories, probably 'CATEGORIES=4' .
You should flag your 2 sets of PE reads as -shortPaired and -shortPaired2, respectively.

Quote:
Originally Posted by Genomics101 View Post

Are the 250bp reads still considered short reads or are they long reads?
See the discussion about this in the velvet manual,

www.ebi.ac.uk/~zerbino/velvet/Manual.pdf

I think it's probably up to you whether you want to consider them long reads or short reads.

see also this thread in the Velvet mailing list archives:
http://listserver.ebi.ac.uk/pipermai...er/001747.html


Quote:
Originally Posted by Genomics101 View Post

Is there a problem now that the read-length is no longer consistent due to trimming?
No.

Last edited by mastal; 12-31-2013 at 04:18 AM.
mastal is offline   Reply With Quote
Old 12-31-2013, 07:50 AM   #3
Genomics101
Member
 
Location: Maryland, USA

Join Date: May 2012
Posts: 60
Default

Thanks very much, the Manual for my version of Velvet was unclear about all these points and I very much appreciate your time on this.
Genomics101 is offline   Reply With Quote
Reply

Tags
de novo assembly, velvet

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 06:58 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO