Hi all,
I am using bwa to align RNA-seq data. Can you please direct me to link or thread that describes the parameter -s under samse command. Why is it working in version 5.7 and not 5.9?
.../bwa-0.5.9/bwa samse -s -n 100 Genome.fasta 07.end1.sai 07.end1.fastq > 07.end1.sam
samse:invalid option -- s
but if i run it in bwa-0.5.7/bwa samse -s -n 100 Genome.fasta 07.end1.sai 07.end1.fastq > 07.end1.sam
[bwa_aln_core] Data structures initialized: 8.43 sec
[bwa_aln_core] 262144 sequences loaded: 0.67 sec
[bwa_aln_core] convert 262144 sequences to sequence coordinate: 4.21 sec
[bwa_aln_core] refine gapped alignments for 262144 sequences: 0.85 sec
[bwa_aln_core] print alignments for 262144 sequences: 2.51 sec
[bwa_aln_core] 262144 sequences have been processed.
......
I am using bwa to align RNA-seq data. Can you please direct me to link or thread that describes the parameter -s under samse command. Why is it working in version 5.7 and not 5.9?
.../bwa-0.5.9/bwa samse -s -n 100 Genome.fasta 07.end1.sai 07.end1.fastq > 07.end1.sam
samse:invalid option -- s
but if i run it in bwa-0.5.7/bwa samse -s -n 100 Genome.fasta 07.end1.sai 07.end1.fastq > 07.end1.sam
[bwa_aln_core] Data structures initialized: 8.43 sec
[bwa_aln_core] 262144 sequences loaded: 0.67 sec
[bwa_aln_core] convert 262144 sequences to sequence coordinate: 4.21 sec
[bwa_aln_core] refine gapped alignments for 262144 sequences: 0.85 sec
[bwa_aln_core] print alignments for 262144 sequences: 2.51 sec
[bwa_aln_core] 262144 sequences have been processed.
......
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