Rsubread: Aligning multiple single and paired-end reads from multiple files (lanes)

Question

[schaeferchristina15]

Hello,

I am new to bioinformatics and looking for some help. I have 27 files from an Illumina output. There are 4 paired end and 23 single read files. I am trying to align them using Rsubread in R directly.

I want to align all of the files at once using a code similar to this:

align(index = "reference_index", readfile1="/path to file/forward_reads_list",readfile2="/path to_file/reverse_reads_list", input_format="FASTQ", output_file="rsubread.bam", type = "dna)

Can I use a single function to align both the single read and paired-end reads? Or do I have to do this separately? Further, if I do have to do two separate functions, how do I merge them later on?

The ultimate goal is to get FASTQ files to align to BAM then pull out variants (using VariantAnnotation) and detect similar SNPs between this dataset and another dataset from DArT sequencing.

Thanks in advance!

[abedkurdi10]

Did you mean you have 27 samples, 4 of them are paired end and 23 are single end?