Greetings!
I plan to do mapping using multiple types of Illumina FASTQ files for the same sample.
I have one set of FASTQs made from a library with 400bp inserts, 100bp reads (trimmed for quality), and processed with the 1.5 pipeline; the second set is 600bp inserts, 250bp reads (trimmed for quality), and processed with the 1.9 pipeline. Because of the trimming process, I have paired-end and single-end FASTQs for each sample as well.
As a result I have 8 FASTQs for mapping, e.g. -
Insert size 400:
Sample1_Illumina_1.5_100bp_R1.fastq.pe
Sample1_Illumina_1.5_100bp_R2.fastq.pe
Sample1_Illumina_1.5_100bp_R1.fastq.se
Sample1_Illumina_1.5_100bp_R2.fastq.se
Insert size 600:
Sample1_Illumina_1.9_250bp_R1.fastq.pe
Sample1_Illumina_1.9_250bp_R2.fastq.pe
Sample1_Illumina_1.9_250bp_R1.fastq.se
Sample1_Illumina_1.9_250bp_R2.fastq.se
I have only been mapping with the 100bp/1.5 so far, using BWA, but reading it looks like I should use BWA-MEM if I am using the longer reads. Is it possible to map all of these together?
Thanks!
I plan to do mapping using multiple types of Illumina FASTQ files for the same sample.
I have one set of FASTQs made from a library with 400bp inserts, 100bp reads (trimmed for quality), and processed with the 1.5 pipeline; the second set is 600bp inserts, 250bp reads (trimmed for quality), and processed with the 1.9 pipeline. Because of the trimming process, I have paired-end and single-end FASTQs for each sample as well.
As a result I have 8 FASTQs for mapping, e.g. -
Insert size 400:
Sample1_Illumina_1.5_100bp_R1.fastq.pe
Sample1_Illumina_1.5_100bp_R2.fastq.pe
Sample1_Illumina_1.5_100bp_R1.fastq.se
Sample1_Illumina_1.5_100bp_R2.fastq.se
Insert size 600:
Sample1_Illumina_1.9_250bp_R1.fastq.pe
Sample1_Illumina_1.9_250bp_R2.fastq.pe
Sample1_Illumina_1.9_250bp_R1.fastq.se
Sample1_Illumina_1.9_250bp_R2.fastq.se
I have only been mapping with the 100bp/1.5 so far, using BWA, but reading it looks like I should use BWA-MEM if I am using the longer reads. Is it possible to map all of these together?
Thanks!
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