How many paired FASTQ reads to input for alignment if 4 different SRA IDs belong to one sample? So there are 8 fastqs of the whole genome of a microbe. Should I align in pairs and then merge the BAM or somehow different? Thanks.
Why are there four different SRA IDs? Are you sure it's the same sample? If so most aligners allow input from multiple files (or pairs of files)
I do agree with Asaf, most aligners handle multiple paired-end inputs.
Some of my colleagues deal with multiple paired-end FastQ files and they process them into batches. In your example, it means running 4 different alignments separately. This is pretty efficient if you have an important read number (>100 millions) and light reference (<5 millions bp). Remember that each alignment run will separately load your reference genome so, depending on read number and reference size, it could be interesting to merge FastQ files to load the reference once.
Last important thing: if all the FastQ files came from the same sequencing run (and same lane), then merge BAM files before removing PCR duplicates so they will be correctly removed.
Cheers.
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Why are there four different SRA IDs? Are you sure it's the same sample? If so most aligners allow input from multiple files (or pairs of files)