SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
MIRA 4.0 denovo PacBio FastQ haudi Bioinformatics 12 08-01-2014 12:08 AM
For MAQ: Is there a Tool to convert sanger-format fastq file to illumina-fotmat fastq byb121 Bioinformatics 6 12-20-2013 01:26 AM
PacBio RS quality score output definition (FASTQ) vamiyn Pacific Biosciences 3 07-16-2013 02:44 AM
Split Large FASTQ file in small FASTQ files with user defined number of reads Windows deepbiomed Bioinformatics 3 04-04-2013 07:14 AM
Reduce file size after Illumina FASTQ to Sanger FASTQ conversion? jjw14 Illumina/Solexa 2 06-01-2010 04:35 PM

Reply
 
Thread Tools
Old 12-07-2014, 08:47 AM   #1
Fad2012
Member
 
Location: UK

Join Date: Sep 2012
Posts: 61
Default how to get the fastq file from bax.h5 pacbio

Hello guys

Recently I have received my PacBio files from the company, which contain the sequencing results. The files are compressed (tar.bz2), when i extracted the file, I found only one file (name_of_the_file.bax.h5), I was wondering what would be the best way to analyse the file, as I am interested in the fastq file. How could i extract the fastq file?

Many thanks
Fad2012 is offline   Reply With Quote
Old 12-08-2014, 07:02 AM   #2
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 322
Default

What kind of analysis are you running on the data, you often need to run through some PacBio specific software before getting data that can be analysed using standard tools. Minimally PacBio's filtering pipeline should be used to generate fastq.
PacBio h5 format
Simple tool for manipulating PacBio h5 files
rhall is offline   Reply With Quote
Old 12-08-2014, 07:42 AM   #3
Fad2012
Member
 
Location: UK

Join Date: Sep 2012
Posts: 61
Default

Thanks rhall

I am interested in the consensus subreads, fastq. I want to align against known reference for SNP detection

Many thanks
Fad2012 is offline   Reply With Quote
Old 12-08-2014, 08:44 AM   #4
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 322
Default

If you don't want to install the full SMRT Analysis system, I would at least use pbalign to align the data, which can use the bax.h5 files, then use quiver to call SNPs, you will get much better results than using other aligners of consensus callers.
rhall is offline   Reply With Quote
Old 12-09-2014, 03:03 PM   #5
Fad2012
Member
 
Location: UK

Join Date: Sep 2012
Posts: 61
Default

Thanks very much Rhall, I will try this. Much appreciated.
Fad2012 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 05:26 PM.


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