[ikrier]

bwa samse ../Mouse_genome.fa tags_all.sai tags_all.fastq > tags_all.sam

[nilshomer]

bwa samse ../Mouse_genome.fa tags_all.sai tags_all.fastq > tags_all.sam

What was your aln command? Are you running this on Illumina or SOLiD reads?

[ikrier]

bwa aln ../Mouse_genome.fa tags_all.fastq > tags_all.sai

[DNAANDDAN]

edition of BWA is concern

what's is your edition of BWA ?
BWA is perfect for Solexa reads, but have some bug for Solid reads. the reads on mins strand have a complentary sequencse ,both single and pair-end reads are have this problem, from some edition of BWA.
use 4.9 try again, it is stable for my result.

Thanks, Chipper. I have not been able to attach it for some reason.

Regarding the NGS exercise, I might have done something wrong at some step then. There wasn't any error or warning along the way, so there was no clue. I tried to post the same question on the samtools-help list. I am copying it below and see if it helps you see my question better. Thanks in advance.

Can someone provide me some pointers regarding SAM format in color space and correct ways to use samtools for processing such SAM files, especially for SNP and indel calling? I looked everywhere but could not find any documentations.

Specifically, as an exercise, here is what I did:

- Simulated some SOLiD reads using wgsim (-c option) from a reference sequence.
- Generated the bwa index with the following command: bwa index -c ref.fa -a is
- Align the reads (in fastq format) back to the reference sequence using bwa:
bwa aln -c ref.fa r1.fq > r1.sai
bwa samse ref.fa r1.sai r1.fq > r1.sam

And I ran the usual faidx, import, sort, index, and pileup commands of samtools and they went smoothly with no errors or warnings. I can view it with samtools tview. Nonetheless, the pileup file just does not make sense to me, as the consensus sequence is almost different to the reference sequence at every position. And, tview seems to be showing the reads still in color space (double encoded?), which is hard or impossible to interpret for me.

[ikrier]

I'm removing my post here because it's not about Solid reads...