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Old 11-28-2011, 02:21 AM   #1
Location: spain

Join Date: Feb 2011
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Default Bfast alignement with paired end reads in separate files


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:
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:

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

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,
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Old 11-28-2011, 05:22 PM   #2
Nils Homer
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Test it out to see what happens. You should be pleasantly surprised.
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Old 11-29-2011, 08:49 AM   #3
Location: spain

Join Date: Feb 2011
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Unfortunately, I think it does not work, the bfast localign seems to take into account only the second passed .bmf file:

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:
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.

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alignement, bfast, paired end reads

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