Hi,
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,
Regards,
Ramzi
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,
Regards,
Ramzi
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