Mapping paired end and single end reads together
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6.2 years ago
RT ▴ 350

Hi Everyone,

I have my raw data as two paired end reads file (one for left and one for right reads) plus a file where I have only single end reads. I am wondering if it is possible to align all this data to the reference genome?

Thanks.

mapping • 4.9k views
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Yes, it is possible. Which kind of data do you have? RNASeq or DNA?

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Whether this is possible in a single command is completely dependent on the aligner you're using.

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I have DNA seq data and I want to use bwa.

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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???

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6.2 years ago
Gabriel R. ★ 2.8k

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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I am wondering if it would be appropriate to do the following: 1) map the paired end and single end read data individually 2) sort the data 3) Merge both the bam files (single end+paired end).

Please suggest!

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That's perfectly fine.

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I would do this instead:

1) merge both the paired and unpaired using samtools cat

2) pipe into network-aware-bwa

This gives you a single mapping step and does not require additional files.

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Thanks Samuel. I will try this. 

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you need libzeromq to install the bwa package. You can get it via apt-get install

 

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