SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Some chromosomes missing in bwa-output (http://seqanswers.com/forums/showthread.php?t=44407)

robinweide 06-21-2014 11:22 AM

Some chromosomes missing in bwa-output
 
Hello!

I have fasta-files, resulting from a de novo assembly. When I map pe-reads to these fastas with bwa-mem (default options), it does not output all the fasta-entries: when looking at the bam-file and extracting the third column, not all fasta-ids can be found....

Is this because bwa-mem with default options does not output non-convered chromosomes? Or is there something else?

Many, many thanks!

dpryan 06-21-2014 12:01 PM

Are they all in the header?


All times are GMT -8. The time now is 03:47 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.