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Old 03-10-2012, 09:24 PM   #1
niteesh.prasad
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Default Using samtools to analyze bwa output

I have a query file with 70,000 lines of sequences and when I do the
Code:
bwasw
each sam output file is about 35 mb and obviously contains all the sequence lines. I need to perform the alignment on about 1000 files, so you can imagine that I don't want to have 35 gigs worth of output to sort.

I am trying to get rid of the non-aligned reads from the SAM output file ans I searched through forums and tried the following code with no avail.

Code:
./samtools view -bS -f 4 testing.sam > output.bam
All my sam files give the following error:

Code:
[samopen] SAM header is present: 1 sequences.
[sam_read1] reference '0' is recognized as '*'.
Parse warning at line 3: mapped sequence without CIGAR
Parse error at line 3: missing colon in auxiliary data
Aborted (core dumped)

Here's what a part of my sam files looks like


Code:
@SQ	SN:gi|89106884|ref|AC_000091.1|	LN:4646332

	4	*	0	0	*	*	0	0	<CGTAAAAAGGA> 	*
	4	*	0	0	*	*	0	0	<TAGCCGTAGGG>   *
I'd appreciate help with this!
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Old 03-11-2012, 08:40 AM   #2
nilshomer
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There's no read name in the SAM records you list.
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Old 03-11-2012, 09:10 AM   #3
niteesh.prasad
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But this is the output I get from bwa. how should i fix this?
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Old 03-11-2012, 09:21 AM   #4
nilshomer
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Post the BWA help mailing list. It looks like a bug to me. Make sure you include a test case.
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Old 03-11-2012, 09:26 AM   #5
niteesh.prasad
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Before I do that, I want to make sure I am not wrong. Here is the code I used for the bwa:

Code:
./bwa bwasw INDEXES/AC_000091.fna QUERY/635plus104_500bp_reads.fasta > results.sam
The input AC_000091.fna was the indexes created with the following command:

Code:
./bwa index AC_000091.fna "AC_000091.fna";
and the query file was a FASTA sequence file.

So, in theory this should have worked?
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