I aligned a fastq file to a refseq data base successfully as follows:
create an index:
bwa index -p RefSeqbwaidx -a bwtsw /mnt/fred/home/efoss/gene_databases/refGene.txt.07Jun2010.fa
(
The refGene.txt.07June2010.fa file has a format like this:
>NM_002697
CGGAGGAGCAGCGAGTCAAGATGAGAGTTCAGCCGCGGCGGCAGCAGCAGCAGACTGGAAAAGTAAGAAGAGCTTTCCTGCCTTTTTAATTACCAAACTA
CTCTCAGTTTTCAATGAATCAGTTCAAAGAAAGAATGCAGTCTTTCTATACCTGACTCAAGAATGAACAATCCGTCAGAAACCAGTAAACCATCTATGGA
GAGTGGAGATGGCAACACAGGCACACAAACCAATGGTCTGGACTTTCAGAA
)
I align my reads:
bwa aln -t 6 RefSeqbwaidx /mnt/fred/home/efoss/sequence_files/FASTQ_files/sequence_r1.fq > sequence_r1.fq.bwa
and I convert the output to SAM format:
bwa samse RefSeqbwaidx sequence_r1.fq.bwa /mnt/fred/home/efoss/sequence_files/FASTQ_files/sequence_r1.fq > sequence_r1.fq.sam
I look into the SAM file and everything looks good. Now I go to align the corresponding "r2" file from the same experiment:
bwa aln -t 6 RefSeqbwaidx /mnt/fred/home/efoss/sequence_files/FASTQ_files/sequence_r2.fq > sequence_r2.fq.bwa
The alignment takes a similar amount of time, the messages reported back as the computer is working look the same, but then in the end my sequence_r2.fq.bwa file is empty. Does anyone have an idea about what is going on?
Thank you.
Eric
create an index:
bwa index -p RefSeqbwaidx -a bwtsw /mnt/fred/home/efoss/gene_databases/refGene.txt.07Jun2010.fa
(
The refGene.txt.07June2010.fa file has a format like this:
>NM_002697
CGGAGGAGCAGCGAGTCAAGATGAGAGTTCAGCCGCGGCGGCAGCAGCAGCAGACTGGAAAAGTAAGAAGAGCTTTCCTGCCTTTTTAATTACCAAACTA
CTCTCAGTTTTCAATGAATCAGTTCAAAGAAAGAATGCAGTCTTTCTATACCTGACTCAAGAATGAACAATCCGTCAGAAACCAGTAAACCATCTATGGA
GAGTGGAGATGGCAACACAGGCACACAAACCAATGGTCTGGACTTTCAGAA
)
I align my reads:
bwa aln -t 6 RefSeqbwaidx /mnt/fred/home/efoss/sequence_files/FASTQ_files/sequence_r1.fq > sequence_r1.fq.bwa
and I convert the output to SAM format:
bwa samse RefSeqbwaidx sequence_r1.fq.bwa /mnt/fred/home/efoss/sequence_files/FASTQ_files/sequence_r1.fq > sequence_r1.fq.sam
I look into the SAM file and everything looks good. Now I go to align the corresponding "r2" file from the same experiment:
bwa aln -t 6 RefSeqbwaidx /mnt/fred/home/efoss/sequence_files/FASTQ_files/sequence_r2.fq > sequence_r2.fq.bwa
The alignment takes a similar amount of time, the messages reported back as the computer is working look the same, but then in the end my sequence_r2.fq.bwa file is empty. Does anyone have an idea about what is going on?
Thank you.
Eric