|
|
|
|||||||
Similar Threads
|
||||
| Thread | Thread Starter | Forum | Replies | Last Post |
| BWA output bitwise flag for mapped/unmapped reads | wenhuang | Bioinformatics | 1 | 08-29-2011 03:54 PM |
| how do I output the CS tag for BWA align of SOLID reads? | KevinLam | Bioinformatics | 16 | 07-23-2011 10:06 PM |
| cufflinks hates my long reads: segmentation faults on bwa output | dagarfield | Bioinformatics | 1 | 02-03-2011 07:20 AM |
| Does output_file of bwa-sw contain unmapping reads? | louis7781x | Bioinformatics | 0 | 11-02-2010 03:18 AM |
| sam output from bwa for SOLiD reads in colorspace? | nisha | SOLiD | 19 | 01-07-2010 04:05 AM |
 |
|
|
Thread Tools |
11-02-2010, 07:10 AM
|
#1 |
|
Member
Location: Hong Kong Join Date: Oct 2010
Posts: 74
|
Does output-file of bwa-sw contain unmapping reads?
Hello everyone,I want to know when we use bwa-sw to alignment,Does its output.sam contain "non-mapping reads"? Because I use default to align 454 against human genomes,output.sam using samtools transfer to bam;and use the command "samtool view f -4 <output.bam>" . It doesn't show any non-mapping reads.
If anyone know the answer,please let me know!! thanks!!! Best regard!! |
|
|
|
04-06-2011, 07:25 AM
|
#2 |
|
Junior Member
Location: usa Join Date: Dec 2010
Posts: 6
|
f -4 means filter unmapped reads and keep the mapped reads which are with flag 0 or 16.
Since you filter the output, you couldn't see any unmapped reads.
__________________
wwq 
|
|
|
|
|
| Thread Tools | |
|
|
