Hi,
I am trying to use BWA for analysing human whole exome PE data (Illumina HiSeq) for the first time.
I downloaded the hg19 genome as a reference as indexed it with bwa index.
Then aligned with bwa aln with the following format of command (for eacg fastq file):
nohup bwa aln ~/work_area/hg19_genome/hg19_chromFa.tar.gz SG1177_2_sequence.txt > SG1177_2_aln_sa.sai &
from the ~10Gb fastq files I got ~1.3 Gb sai files.
But when I am trying to use sampe to get the sam files, it doesn't work, and the output file contains the following comments:
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bwa_read_seq] the maximum barcode length is 63.
then the list of chromosomes
and end.
Here is the sampe command I used:
nohup bwa sampe ~/work_area/hg19_genome/hg19_chromFa.tar.gz SG1177_1_aln_sa.sai SG1177_2_aln_sa.sai SG1177_1_sequence.txt SG1177_2_sequence.txt &
What did I do wrong?
Many thanks in advance!
I am trying to use BWA for analysing human whole exome PE data (Illumina HiSeq) for the first time.
I downloaded the hg19 genome as a reference as indexed it with bwa index.
Then aligned with bwa aln with the following format of command (for eacg fastq file):
nohup bwa aln ~/work_area/hg19_genome/hg19_chromFa.tar.gz SG1177_2_sequence.txt > SG1177_2_aln_sa.sai &
from the ~10Gb fastq files I got ~1.3 Gb sai files.
But when I am trying to use sampe to get the sam files, it doesn't work, and the output file contains the following comments:
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bwa_read_seq] the maximum barcode length is 63.
then the list of chromosomes
and end.
Here is the sampe command I used:
nohup bwa sampe ~/work_area/hg19_genome/hg19_chromFa.tar.gz SG1177_1_aln_sa.sai SG1177_2_aln_sa.sai SG1177_1_sequence.txt SG1177_2_sequence.txt &
What did I do wrong?
Many thanks in advance!
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