Question: How To Use Illumina 1.8 Reads In Stampy?
0
gravatar for lyfsa
8.0 years ago by
lyfsa30
lyfsa30 wrote:

Hi,

Is it possible to use illumina 1.8 reads in Stampy??

• 2.0k views
ADD COMMENTlink modified 8.0 years ago by Istvan Albert ♦♦ 84k • written 8.0 years ago by lyfsa30
0
gravatar for Istvan Albert
8.0 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

Yes.

Illumina 1.8 corresponds to Sanger encoding

Starting in Illumina 1.8, the quality scores have basically returned to the use of the Sanger format (Phred+33)

The Stampy manual states that:

By default Stampy assumes that the quality scores use Sanger encoding (score 0 is '!', ascii 33), and use the phred (=log p) scale, not the logit (=log p/(1-p)) scale.

ADD COMMENTlink written 8.0 years ago by Istvan Albert ♦♦ 84k

yes but stampy is throwing error when used with --bwaoptions.

ADD REPLYlink written 8.0 years ago by lyfsa30

you will need to post the error message.

ADD REPLYlink written 8.0 years ago by Istvan Albert ♦♦ 84k

stampy: Error: Mixed single- and paired-end in input; BWA can't handle this, but when I run stampy without --bwaoption, stampy works.

ADD REPLYlink written 8.0 years ago by lyfsa30

so your question really is that about how to use stampy with an input that contains both single and paired end reads. You should ask that question separately and make sure to include all relevant details for example where you got your input files from so that people can help you.

ADD REPLYlink written 8.0 years ago by Istvan Albert ♦♦ 84k

I have pair end reads from illumina 1.8 only. But as both illumina1.8 and sanger uses sanger format, Stampy with --bwaoption is not able to distinguish illumina 1.8 reads as pair files and throws an error. I use stampy with default (i.e sanger) and -M option. But seems like this is a problem of stampy.

ADD REPLYlink written 8.0 years ago by lyfsa30

bwaoptions just passes additional options to the bwa aligner. It should have nothing to do with quality string encoding. Your data is not paired in the way that the tools expects, perhaps you have reads in one file that are missing in the second file, a common error if the files were filtered separately.

ADD REPLYlink written 8.0 years ago by Istvan Albert ♦♦ 84k

Might be the case. How can I check for missing reads in two files? This is a first time I am using Illumina 1.8 reads for mapping. Before I used stampy with --bwaoption in illumina 1.3 reads and there was no error.

ADD REPLYlink written 8.0 years ago by lyfsa30

You will need to ask this as a new, different question regarding paired data. I am quite certain that the problems are with your data and not the options.

ADD REPLYlink written 8.0 years ago by Istvan Albert ♦♦ 84k
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