Mapping paired end and single end reads together
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Is this genomic? Is BWA ok? You could transform the data into BAM and use this: https://github.com/udo-stenzel/network-aware-bwa
It's a custom version of BWA that eats BAM (paired and single reads) and spits out BAM.
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Ram
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Gabriel R.
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Gabriel R.
That's perfectly fine.
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Devon Ryan
I would do this instead:
- Merge both the paired and unpaired using
samtools cat - Pipe into network-aware-bwa
This gives you a single mapping step and does not require additional files.
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Ram
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Gabriel R.
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Gabriel R.
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Yes, it is possible. Which kind of data do you have? RNASeq or DNA?
Whether this is possible in a single command is completely dependent on the aligner you're using.
I have DNA seq data and I want to use bwa.
I was thinking of doing the same thing but won't we be duplicating reads, as we will be counting the same read twice - once from paired end fastq and once from the single read fastq???