Mapping multiple FASTQ data types using BWA?

Genomics101 · 01-02-2014, 08:33 AM

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!

adamdeluca · 01-02-2014, 12:54 PM

I would map separately for each insert size, then merge the resulting bams for further analysis.

dpryan · 01-02-2014, 12:55 PM

No, don't map them together. Also, bwa mem doesn't support illumina 1.5.

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01-02-2014, 08:33 AM	#1
Genomics101 Member Location: Maryland, USA Join Date: May 2012 Posts: 60	Mapping multiple FASTQ data types using BWA? 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!

01-02-2014, 12:54 PM	#2
adamdeluca Member Location: Iowa City, IA Join Date: Jul 2010 Posts: 95	I would map separately for each insert size, then merge the resulting bams for further analysis.

01-02-2014, 12:55 PM	#3
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	No, don't map them together. Also, bwa mem doesn't support illumina 1.5.