SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
random downloading of .sff file paa6 Introductions 19 02-12-2014 07:07 PM
Split SFF file by Adaptors HeidiLee 454 Pyrosequencing 3 08-06-2012 05:42 AM
Help!sff-dump error , convert sra to sff jimbeibei Bioinformatics 1 03-16-2012 10:20 AM
sff file problems clostridium40 454 Pyrosequencing 8 08-02-2011 03:12 AM
Difference between .sff files and .fq file edge Bioinformatics 3 10-04-2009 06:30 PM

Reply
 
Thread Tools
Old 04-27-2014, 10:17 PM   #1
chayan
Member
 
Location: USA

Join Date: Nov 2012
Posts: 51
Default counting the details of a .SFF file

Hii All,

Is there a way/utility to get the details of any .SFF file?? I want to
calculate the total no of reads, bases, and Q20 bases in my Ion .SFF file.
I mean utilities which are there for FASTQ..i am very much new to this..

thanx for any help

Regards

chayan
chayan is offline   Reply With Quote
Old 04-27-2014, 10:47 PM   #2
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 628
Default

Convert the file to fastq (e.g. with http://bioinf.comav.upv.es/seq_crumbs/ or any other tool). Then just use the desired tools for fastq.

best,
Sven
sklages is offline   Reply With Quote
Old 04-28-2014, 09:53 AM   #3
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

See also http://seqanswers.com/forums/showthread.php?t=42868 where sffinfo and other tools are suggested.
maubp is offline   Reply With Quote
Reply

Tags
fastqc, fastx-toolkit, iontorrnet, sff_extract

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 07:37 PM.


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