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BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data
http://pellegrini.mcdb.ucla.edu/BS_Seeker2/
MIT License
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Base Qualities #7

Closed aheravi closed 7 years ago

aheravi commented 8 years ago

Hi, In BSseeker2, it seems to me there is no base quality attached to the reads. Is that true?

samtools view EX0001_bsSeeker2.kayrotypic.sorted.ReadGroup.bam | cut -f11 | head -1 *

BSSeeker commented 8 years ago

Yes, you are right.

BS-Seeker2 would not consider base quality, but in fact consider number of mismatches.

From our experiences, no significant difference to include the quality or not when mapping.

You may trace back to fastq/qseq file using reads ID for base quality information. And I would like to hear from you if any concern on this issue or related.

Best, Weilong

在 2016-05-12 06:05:30，"aheravi" notifications@github.com 写道：

Hi, In BSseeker2, it seems to me there is no base quality attached to the reads. Is that true?

samtools view EX0001_bsSeeker2.kayrotypic.sorted.ReadGroup.bam | cut -f11 | head -1 *

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aheravi commented 8 years ago

Well, I am trying to run BisSNP on the bam and need those base qualities for the recalibration process. Thanks, Ali

BSSeeker commented 8 years ago

Hi Ali,

The easiest way is to set the column as best for all bases.

Also to retrieve the raw data for quality.

If BS-Seeker2 supports quality in the future, I'll let you know.

Best, Weilong

At 2016-05-12 08:00:37, "aheravi" notifications@github.com wrote:

Well, I am trying to run BisSNP on the bam and need those base qualities for the recalibration process. Thanks, Ali

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