I have sequenced a 6MB region of a single chromosome of the dog genome (targeted capture).
At first I used a fasta file from GenBank of the particular chromosome as a reference sequence to map my reads. I indexed the ref sequence and ran bwa aln, which created a .sai file of about 330 MB for each read. I subsequently ran bwa sampe, which succesfully generated a 9.7 GB .sam file from the paired-end reads.
After this I was recommended to map my reads to the complete genome. So I downloaded the following fasta files from ensemble: each chromosome (1-38), MT, and non-chromosomal DNA and merged the files by cat chr1 chr2 chr3...> mergedFasta.fa. I indexed the fasta file by bwa index and then I ran bwa aln to create .sai files. I got no error messages but noticed that the output file now was 60MB (compared to the 330 .sai file I got when mapping to the single chr GenBank file). I tried to run bwa sampe on the generated .sai files but the program is hanging within 2 minutes. I assume this has to do with the initial creation of the .sai file and the reference FASTA file, but I cant figure out what is wrong? Can somebody help me please?
At first I used a fasta file from GenBank of the particular chromosome as a reference sequence to map my reads. I indexed the ref sequence and ran bwa aln, which created a .sai file of about 330 MB for each read. I subsequently ran bwa sampe, which succesfully generated a 9.7 GB .sam file from the paired-end reads.
After this I was recommended to map my reads to the complete genome. So I downloaded the following fasta files from ensemble: each chromosome (1-38), MT, and non-chromosomal DNA and merged the files by cat chr1 chr2 chr3...> mergedFasta.fa. I indexed the fasta file by bwa index and then I ran bwa aln to create .sai files. I got no error messages but noticed that the output file now was 60MB (compared to the 330 .sai file I got when mapping to the single chr GenBank file). I tried to run bwa sampe on the generated .sai files but the program is hanging within 2 minutes. I assume this has to do with the initial creation of the .sai file and the reference FASTA file, but I cant figure out what is wrong? Can somebody help me please?
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