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-   -   conver bam to fastq (http://seqanswers.com/forums/showthread.php?t=73745)

xthua 01-22-2017 05:22 PM

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

WhatsOEver 01-22-2017 11:43 PM

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 01:37 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 12:47 PM

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


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