Question: Mapping paired end and single end reads together
0
gravatar for RT
3.5 years ago by
RT330
European Union
RT330 wrote:

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 • 3.4k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by RT330

Yes, it is possible. Which kind of data do you have? RNASeq or DNA?

ADD REPLYlink written 3.5 years ago by iraun3.4k

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

ADD REPLYlink written 3.5 years ago by Devon Ryan81k

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

ADD REPLYlink written 3.5 years ago by RT330

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. 

ADD REPLYlink written 3.5 years ago by Gabriel R.2.4k
1

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!

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by RT330
1

That's perfectly fine.

ADD REPLYlink written 3.5 years ago by Devon Ryan81k
1

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.

ADD REPLYlink written 3.5 years ago by Gabriel R.2.4k

Thanks Samuel. I will try this. 

ADD REPLYlink written 3.5 years ago by RT330

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

 

ADD REPLYlink written 3.5 years ago by Gabriel R.2.4k
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