bwa samse -s parameter

[rahul]

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.
......

[swbarnes2]

I don't have that version, but neither 0.4.9 nor 0.5.8a have a -s option for samse. What was -s supposed to do in samse in v. 0.5.7?

[Richard Finney]

Please check again:

I get -s as invalid in bwa-0.5.7 ...

-bash-3.00$ bwa-0.5.7/bwa samse -s
samse: invalid option -- s

There appears to be no -s parameter to bwa samse in recent versions ...

grep getopt ../bwa*/bwase.c
../bwa-0.5.7/bwase.c: while ((c = getopt(argc, argv, "hn:f:")) >= 0) {
../bwa-0.5.8a/bwase.c: while ((c = getopt(argc, argv, "hn:f:")) >= 0) {
../bwa-0.5.8c/bwase.c: while ((c = getopt(argc, argv, "hn:f:")) >= 0) {
../bwa-0.5.9/bwase.c: while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {
../bwa-0.6.0/bwase.c: while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {

So, it's only looking for h(help),n(n_occ),f(outbam) and later r(readgroup)

[rahul]

Thanks for the reply. I am not sure what -s does. It is a step in RNASeq data analysis pipeline. I will update my post once i find what the parameter stands for.

Thank you,

Rahul

[kopi-o]

Are you sure you want to use bwa to map RNA-seq data to a genomic reference (Genome.fasta)? It will miss splicing ... I would either map to a transcriptome reference or switch to a different tool.

[rahul]

Sorry: It is a customized parameter

They have customized the bwa and the parameter was to implement the customized step. I should have contacted the author before posting it here. Sorry for the trouble.

[rahul]

Are you sure you want to use bwa to map RNA-seq data to a genomic reference (Genome.fasta)? It will miss splicing ... I would either map to a transcriptome reference or switch to a different tool.

Thanks for the advice. It is mapping to the transcriptome. I did not display the actual file names. Sorry again.