conver bam to fastq

xthua · 01-22-2017, 06:22 PM

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
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

WhatsOEver · 01-23-2017, 12:43 AM

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?

rhall · 01-23-2017, 02:37 PM

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.

cement_head · 09-29-2019, 01:47 PM

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

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01-22-2017, 06:22 PM	#1
xthua Junior Member Location: sweden Join Date: Apr 2013 Posts: 2	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 + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

01-23-2017, 12:43 AM	#2
WhatsOEver Senior Member Location: Germany Join Date: Apr 2012 Posts: 215	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?

01-23-2017, 02:37 PM	#3
rhall Senior Member Location: San Francisco Join Date: Aug 2012 Posts: 322	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.

09-29-2019, 01:47 PM	#4
cement_head Senior Member Location: Oxford, Ohio Join Date: Mar 2012 Posts: 253	May this will help? https://github.com/PacificBiosciences/bam2fastx