Convert chimeric.out.sam to chimeric.out.junction

[Benjy Jek Yang Tan]

Hi Alex,

Good day to you. Thank you very much for your work.

I would like to ask if there is any way I can convert my chimeric.out.sam file to chimeric.out.junction by myself instead of using the chimeric.out.junction generated by STAR. 

This is because I need to apply some filters on the SAM file first (such as mapping quality filtering) and I couldn't do that with the chimeric.out.junction file.

Hope to hear back from you soon. 

Thank you very much.

Best regards,

Benjy

[Alexander Dobin]

Hi Benjy,

you would have to write your own script to do that, STAR does not have an option to do this.

However, an easier option would be to parse the two file simultaneously, since the .junction file has exactly one line per read for all the reads in the .sam file,

and the 10th columns in the .junction file contains the read ID - which is 1st column in the .sam file.

So if you decide to filter some reads from the .sam files, you can simply remove the corresponding lines from the .junction file.

Cheers

Alex