Bfast alignement with paired end reads in separate files

david.tamborero · 11-28-2011, 02:21 AM

Hello,

I am dealing with Illumina paired end reads (100 + 100) and I am trying to align them by using bfast. The point is that they are in separate files, and I am wondering which is the best way to proceed. My attempt:

1. bfast match:

Code:

bfast match -f hg19.fa -A 0  -g -r reads_file_pair_1.fastq.gz -i 1 -K 8 -M 128 -w 0 > pair_1.bmf
bfast match -f hg19.fa -A 0  -g -r reads_file_pair_2.fastq.gz -i 1 -K 8 -M 128 -w 0 > pair_2.bmf

2. bfast localalign:

Code:

bfast localalign -f hg19.fa -m pair_1.bmf -m pair_2.bmf -n 4 -A 0 -U > sample.baf

3. bfast postprocess

Code:

bfast postprocess -i sample.baf -f hg19.fa -a 3 -z -A 0 -R -O 1 -n 4 -U | gzip > sample.sam.gz

I am concerned specially in step 2; I am used to use two .bmf files (one per paired-end) in the bfast localign command when they have been outputted by the bfast bwaaln command (using "-1" and "-2" arguments), but I've never done so with bafst match output files.

Tahnk you very much in advance,

nilshomer · 11-28-2011, 05:22 PM

Test it out to see what happens. You should be pleasantly surprised.

david.tamborero · 11-29-2011, 08:49 AM

Unfortunately, I think it does not work, the bfast localign seems to take into account only the second passed .bmf file:

Code:

bfast localalign -f hg19.fasta -m dummy_p1.bmf -m dummy_p2.bmf -n 4 -A 0 -U > dummy.baf

The stdoutput when executing this command:

Code:

************************************************************
Printing Program Parameters:
programMode:			[ExecuteProgram]
fastaFileName:			hg19.fasta
matchFileName:			dummy_p2.bmf
matchFileNameOne:		[Not Using]
matchFileNameTwo:		[Not Using]
scoringMatrixFileName:		[Not Using]
ungapped:			[Not Using]
unconstrained:			[Using]
space:				[NT Space]
startReadNum:			1
endReadNum:			2147483647
offsetLength:			20
maxNumMatches:			384
avgMismatchQuality:		10
numThreads:			4
queueLength:			10000
timing:				[Not Using]
************************************************************

And effectively, I've checked the .sam file obtained after the bfast postprocess step and the aligned reads are only those of the second "end-reads" file.

Am I doing something wrong? Btw, I am using the bfast+bwa-0.6.4e.

Thanks,
David

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11-28-2011, 02:21 AM	#1
david.tamborero Member Location: spain Join Date: Feb 2011 Posts: 60	Bfast alignement with paired end reads in separate files Hello, I am dealing with Illumina paired end reads (100 + 100) and I am trying to align them by using bfast. The point is that they are in separate files, and I am wondering which is the best way to proceed. My attempt: 1. bfast match: Code: bfast match -f hg19.fa -A 0 -g -r reads_file_pair_1.fastq.gz -i 1 -K 8 -M 128 -w 0 > pair_1.bmf bfast match -f hg19.fa -A 0 -g -r reads_file_pair_2.fastq.gz -i 1 -K 8 -M 128 -w 0 > pair_2.bmf 2. bfast localalign: Code: bfast localalign -f hg19.fa -m pair_1.bmf -m pair_2.bmf -n 4 -A 0 -U > sample.baf 3. bfast postprocess Code: bfast postprocess -i sample.baf -f hg19.fa -a 3 -z -A 0 -R -O 1 -n 4 -U \| gzip > sample.sam.gz I am concerned specially in step 2; I am used to use two .bmf files (one per paired-end) in the bfast localign command when they have been outputted by the bfast bwaaln command (using "-1" and "-2" arguments), but I've never done so with bafst match output files. Tahnk you very much in advance,

11-28-2011, 05:22 PM	#2
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	Test it out to see what happens. You should be pleasantly surprised.