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?
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???
Is this genomic ? Is BWA ok ? You could transform the data into BAM and use this :
It's a custom version of BWA that eats BAM (paired and single reads) and spits out BAM.
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).
That's perfectly fine.
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.
Thanks Samuel. I will try this.
you need libzeromq to install the bwa package. You can get it via apt-get install
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