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:
2. bfast localalign:
3. bfast postprocess
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,
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
Code:
bfast localalign -f hg19.fa -m pair_1.bmf -m pair_2.bmf -n 4 -A 0 -U > sample.baf
Code:
bfast postprocess -i sample.baf -f hg19.fa -a 3 -z -A 0 -R -O 1 -n 4 -U | gzip > sample.sam.gz
Tahnk you very much in advance,
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