Hello
I used bowtie to map sequencing reads:
I would like to make a fastq file from the reads with at least one reported alignment [(9391748 (77.72%)].
Converting sam to bam and then using the samtools view with the -F 4 option gives me the Reported 30293838 alignments.
Any suggestions will be appreciated.
Joseph
I used bowtie to map sequencing reads:
Code:
> bowtie ~/hg19 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s)
Converting sam to bam and then using the samtools view with the -F 4 option gives me the Reported 30293838 alignments.
Any suggestions will be appreciated.
Joseph
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