Bam file change chromosome name

You can adjust these settings if you wish. If you zoom in to the sequence level, you will see reads aligned to the anchor sequence with insertions and mismatches highlighted. Pointing a mouse to an individual alignment feature will open a tooltip with a lot of useful information about the alignment, including the CIGAR string, percent identity, and coverage.

Then the steps are similar to scenario 1. Select button on the right that says Add a BAM file. New dialog appears asking about mapping the file to sequences. In order to view the BAM file, the project must contain the sequences e. Note: in case you want to check what sequences are referenced in the BAM file, you can click on Next button in the mapping dialog and see it, and then use Back button to get back to the mapping dialog.

Add a checkmark to the Use Mapping check box, click on the Find Assembly button, and in the Select Assembly dialog type hg Click Next and Finish. SAMTools can take couple of minutes to process this data. The following script is for converting all BAM files in a directory: for B in.

Share this: Twitter Facebook. Like this: Like Loading Leave a Reply Cancel reply Enter your comment here Fill in your details below or click an icon to log in:. Email required Address never made public. I've seen scripts that screwed up the file contents in subtle enough ways to mess up downstream analyses.

Even if you avoid that, you can end up combining data aligned to different genome reference builds, which also ends up affecting analysis results. It's much safer to realign from scratch like KT8 describes. Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password. Post as a guest Name. Email Required, but never shown. Featured on Meta. New post summary designs on greatest hits now, everywhere else eventually. Related 4. Hot Network Questions.

Question feed. Thread Tools. BAM file Hi everyone, I have. Send a private message to ddaneels. Find More Posts by ddaneels. Send a private message to adaptivegenome. Find More Posts by adaptivegenome. Send a private message to dpryan. Find More Posts by dpryan. Send a private message to ffinkernagel. Find More Posts by ffinkernagel. Quote: Originally Posted by ddaneels That would be a way to change the header, but if I'm not mistaking the chromosome numbers are also in the actual read-part of the file.

Quote: Originally Posted by ffinkernagel You are mistaken. Send a private message to xied Find More Posts by xied Send a private message to maubp. Quote: Originally Posted by dpryan Look at the samtools reheader command. Quote: Originally Posted by maubp I don't think that would work. OK - I may have been worrying over nothing then. Quote: Originally Posted by ddaneels my header.