Question: Unexpected Bowtie2 behavior with --phred64 and --phred33 flags
gravatar for Denis
5 months ago by
Denis140 wrote:

I'm stiil not able to figure out how Bowtie2 deal with different Phred quality encoding. In my recent post: enter link description here

genomax pointed me to use --phred64 flag when using Bowtie2 to map Phred+64 encoded reads. I tried both --phred64 and --phred33 flags to map the same reads to reference. All my reads have the same quality score in each position (just short example):


Obiously the reads are Phred+64 encoded. My first command line was:

bowtie2  --very-sensitive --phred64 -x index -U ForAlign.fa.gz -S AlignFullvs_test_64.sam

In the log file i've found:

249631 reads; of these:
  249631 (100.00%) were unpaired; of these:
    6787 (2.72%) aligned 0 times
    199271 (79.83%) aligned exactly 1 time
    43573 (17.45%) aligned >1 times
97.28% overall alignment rate

Further, i used the same command but changed --phred64 to --phred33 flag:

bowtie2  --very-sensitive --phred33 -x index -U ForAlign.fa.gz -S AlignFullvs_test_33.sam

In the log file:

249631 reads; of these:
  249631 (100.00%) were unpaired; of these:
    7132 (2.86%) aligned 0 times
    200810 (80.44%) aligned exactly 1 time
    41689 (16.70%) aligned >1 times
97.14% overall alignment rate

So, as you can see, the overall statistics was almost the same, there were not any errors or at least warnings in both runs. My questions are:

  1. How Bowtie2 can map Phred+64 encoded reads with --phred33 flag without any errors?
    1. Are the both resulted SAM files correct?
alignment software error • 282 views
ADD COMMENTlink modified 5 months ago by Devon Ryan92k • written 5 months ago by Denis140

You can also change the Q scores to phred+33 by using the following program from BBMap suite before mapping: in=your.fq.gz out=new.fq.gz qin=64 qout=33
ADD REPLYlink written 5 months ago by genomax74k
gravatar for Devon Ryan
5 months ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:
  1. The phred scores are only ever used for computing alignment scores in cases where there are mismatches. The alignment score itself will be wrong, but that won't change where the actual resulting alignments are found.
  2. Base qualities in SAM files are defined to be Phred+33, so if you tell bowtie2 the wrong thing the resulting SAM/BAM files will technically be malformed. Whether this is actually a problem is use-case dependent (this is likely only an issue for variant calling).
ADD COMMENTlink written 5 months ago by Devon Ryan92k

Hi Devon Ryan! Many thanks for your reply, it makes things clear. Let me ask just one more question please? I'm wondering how single mismatch with quality "f" (ASCII 102) will be scored in Phred+33 mode?

ADD REPLYlink written 5 months ago by Denis140

It's a mismatch at a high quality base, so it'd be the maximum penalty. This would be the case even if Phred+64 had been used.

ADD REPLYlink modified 5 months ago • written 5 months ago by Devon Ryan92k
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