Viewing the sai file generated using bwa

Question

[Louis Kok]

Hi. I am working on RNA-Seq analysis which was partially done by a researcher who left the team. The only mapping files that I have is the sai files but not the bam files. May I know if there is a way to view the content of the sai files? Thanks in advance.

[h.mon]

Do you still have the fastq files?

[Louis Kok]

Yes. I have the fastq but do not know what the reference it was mapped to.

[h.mon]

Isn't it better to start all over? If you don't know the genome used, I wonder what else you don't know. Do you know if the reads are good quality? Do you know if adapters have been trimmed? Were the reads mapped to a reference genome or transcriptome?

These sai files are output from BWA, which is not an appropriate program to map RNAseq to a reference genome.

[cpad0112]

are you sure that files sai files? They are index files of sam files. See if you have .sam files along with .sai. If you have .sai files only, you can not proceed further.

Answer 1

[noahaus]

I'd checkout the BWA command samse. If you have transcript data such as fastq, then you can save the output of the command as a SAM which can be later on made into a BAM.