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12.2 years ago
lyfsa
▴
30
Hi,
Is it possible to use illumina 1.8 reads in Stampy??
0
Entering edit mode
12.2 years ago
Istvan Albert
101k
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.
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yes but stampy is throwing error when used with --bwaoptions.
you will need to post the error message.
stampy: Error: Mixed single- and paired-end in input; BWA can't handle this, but when I run stampy without --bwaoption, stampy works.
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.
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.
bwaoptionsjust 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.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.
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.