Hello everyone,
I aligned Illumina paired-end data with Mosaik to the hg19. Now, when I wanted to convert the output to a BAM- or SAM-file with MosaikText, the pairing information gets lost. That means in the SAM-file the flag contains no information about pairing (proper pair, mate mapped, etc.) and the columns about mate localization only contain a placeholder (*). So, it looks like a SAM-file for single-end data.
For further analysis with other tools I really need a SAM-file including pairing information. And I don't like to repeat the alignment with another aligner.
Is this a bug or intended? I don't know what might have gone wrong, because the alignment and paired-end read resolution with MosaikSort worked well without any errors.
Hope someone has some ideas and can give some hints. I really appreciate any kind of help! Thanks in advance.
I aligned Illumina paired-end data with Mosaik to the hg19. Now, when I wanted to convert the output to a BAM- or SAM-file with MosaikText, the pairing information gets lost. That means in the SAM-file the flag contains no information about pairing (proper pair, mate mapped, etc.) and the columns about mate localization only contain a placeholder (*). So, it looks like a SAM-file for single-end data.
For further analysis with other tools I really need a SAM-file including pairing information. And I don't like to repeat the alignment with another aligner.
Is this a bug or intended? I don't know what might have gone wrong, because the alignment and paired-end read resolution with MosaikSort worked well without any errors.
Hope someone has some ideas and can give some hints. I really appreciate any kind of help! Thanks in advance.