SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
some help ! BAM to Fastq elitatoun Bioinformatics 12 10-26-2015 03:36 AM
fastq to bam hugh_hang Bioinformatics 10 05-22-2015 12:51 AM
Conver\ variadevang Bioinformatics 1 03-21-2014 02:58 AM
Convert merged BAM back to per lane BAM or FASTQ file danielsbrewer Bioinformatics 6 10-03-2013 07:29 AM
Reverse engineering BAM files: BAM -> FASTQ gene coder Bioinformatics 3 01-03-2012 02:42 PM

Reply
 
Thread Tools
Old 01-22-2017, 05:22 PM   #1
xthua
Junior Member
 
Location: sweden

Join Date: Apr 2013
Posts: 2
Default conver bam to fastq

hi, I try to convert the bam produced by pacbio sequel platform to fastq file. The output file showed the detailed sequence, but the quality values were all "!". both "bamToFastq" and "samtools bam2fq" were used.

@m54061_161228_010008/4194368/0_66
AGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
xthua is offline   Reply With Quote
Old 01-22-2017, 11:43 PM   #2
WhatsOEver
Senior Member
 
Location: Germany

Join Date: Apr 2012
Posts: 215
Default

bam to fastq conversion is actually not something particularly difficult...
Could you paste the corresponding sam record to your example
What about the original data (before alignment); how does this look?
WhatsOEver is offline   Reply With Quote
Old 01-23-2017, 01:37 PM   #3
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 322
Default

Sequel data does not have a per base QV value for raw reads. If you calculate CCS first then the quality values will be meaningfully populated.
rhall is offline   Reply With Quote
Old 09-29-2019, 12:47 PM   #4
cement_head
Senior Member
 
Location: Oxford, Ohio

Join Date: Mar 2012
Posts: 253
Default

May this will help? https://github.com/PacificBiosciences/bam2fastx
cement_head 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 06:06 AM.


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