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Old 07-20-2010, 03:09 AM   #1
Location: Doha, Qatar

Join Date: Oct 2009
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Default Paired-end Bam from single-end aligned sam

I have 2 sam(reverse and farward) files generated by bowtie.
I would like to generate a paired-end bam file from the 2 sam files.
using samtools merge -nr generate only a file with the concatenation of the singles reads from bothb file but do not do the pairing
tried also samtools fixmate but it's not working.
I've looked at the spec for SAM format, in 1.4.4. Storing paired-end reads the following is stated : "A tool is also provided to reconstruct mating information from BAM, although this is done at the cost of intensive computation and large disk space."
Is there any tool that allow to do the pairing of single reads based on the read ID ?
Thanks in advance for your help,

Last edited by ramouz87; 07-20-2010 at 05:20 AM.
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Old 08-17-2011, 06:44 AM   #2
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Location: Helsinki

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Hi everyone!
Did you manage to get an answer for your question dear ramouz87?
I have a similar questions except that I have two .bam files that include the pairs that are mapped, separately. I want to associate the pairs and have the results as a single .bam file.

Does anyone know how that is possible?
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Old 08-17-2011, 10:17 AM   #3
Location: Seattle

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I just came to this site to ask the same question - I have two sam files from Bowtie that come from paired end reads and I want to create one sam or bam file that incorporates the paired end information.

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Old 08-17-2011, 12:22 PM   #4
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Please redo the alignment with a mapper supporting proper paired-end mapping. Merging single-end alignment afterwards always gives you worse results.
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Old 08-17-2011, 12:55 PM   #5
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Location: Seattle, WA

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@ efoss, oghabian, ramouz87

I don't think there's any reasonable way to get from one to the other. The alignments you got by treating the reads as singles are not the same as what you'll get if you align them as paired. You can either redo the alignment as paired (the best solution) or forge ahead with what you've got treating the reads as single end.

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