How to check read are properly paired from SAM file?

jlfmssm · 06-25-2010, 04:07 PM

I am new for NGS data.
How to check reads are properly paired from SAM file?
It is appreciated someone can point me some programs?

Thanks,
Aimin

nilshomer · 06-25-2010, 04:15 PM

Quote:

Originally Posted by jlfmssm

I am new for NGS data.
How to check reads are properly paired from SAM file?
It is appreciated someone can point me some programs?

Thanks,
Aimin

Use 'samtools view -X <in.bam>'. All reads with a capital "P" in the flag field are properly paired.

jlfmssm · 06-25-2010, 05:41 PM

Thanks, I tried, but I got this error:

[aimin@node01 all_sam_data]$ samtools view -X 1382_1.sam/1382_1.sam
[bam_header_read] EOF marker is absent.
[main_samview] fail to read the header.

nilshomer · 06-25-2010, 06:00 PM

Quote:

Originally Posted by jlfmssm

Thanks, I tried, but I got this error:

[aimin@node01 all_sam_data]$ samtools view -X 1382_1.sam/1382_1.sam
[bam_header_read] EOF marker is absent.
[main_samview] fail to read the header.

Use the "-S" flag to specify that you are inputting a SAM file (not a BAM file). Please read the documentation, including the output when no options/input is specified.

jlfmssm · 06-25-2010, 08:13 PM

but I got this:
[aimin@node01 all_sam_data]$ samtools view -S -X 1382_1.sam/1382_1.sam -o 1382_1_test.out
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
What I should do now?

nilshomer · 06-25-2010, 11:23 PM

Quote:

Originally Posted by jlfmssm

but I got this:
[aimin@node01 all_sam_data]$ samtools view -S -X 1382_1.sam/1382_1.sam -o 1382_1_test.out
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
What I should do now?

The lines "no @SQ lines in the header" and "missing header?" should tell you to check the header in the SAM file. Is there one? If not, you have to feed in your reference with the "-T" option.

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06-25-2010, 04:07 PM	#1
jlfmssm Member Location: Boston Join Date: Apr 2010 Posts: 14	How to check read are properly paired from SAM file? I am new for NGS data. How to check reads are properly paired from SAM file? It is appreciated someone can point me some programs? Thanks, Aimin

06-25-2010, 05:41 PM	#3
jlfmssm Member Location: Boston Join Date: Apr 2010 Posts: 14	Thanks, I tried, but I got this error: [aimin@node01 all_sam_data]$ samtools view -X 1382_1.sam/1382_1.sam [bam_header_read] EOF marker is absent. [main_samview] fail to read the header.

06-25-2010, 08:13 PM	#5
jlfmssm Member Location: Boston Join Date: Apr 2010 Posts: 14	but I got this: [aimin@node01 all_sam_data]$ samtools view -S -X 1382_1.sam/1382_1.sam -o 1382_1_test.out [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort! What I should do now?