Dear All,
I hope not to be inopportune with this e-mail, which initially was sent as private message to "maubp". I’m new novice in the world of NGS data sets analysis. I've reading many posts (samtools, seqanswers) about the different few ways that exist to process back SAM/BAM files into the fastq format that the aligners expect. According to my search, I think many of you have posted different suggestions about the challenges that this represents and what we should consider if we plan to perform this action.
Due that this messages were posted about two years ago, some of them older. See links:
As the amount of post is really diverse, and sometimes contradictory among some members, I would appreciate if you could help me to figure out if there are new ways to perform this action to recover the all relevant information, reads IDs and also keep the orphans to be considered as part of the new FASTQ files. If not, could you help me to clarify how can I proceed with this step by step?
I do really need to perform new alignments with the new genome references that have been released recently, but also others that we have generated. Unfortunately for me, I just had access to the bam files obtained from pair ended reeds that were friendly provided by other research groups.
Please apologise me if due to my unfamiliarity, I missed some clue or basic points from previous posts. I also sorry for the long message!!
Many many thanks,
Best regards,
Varo
I hope not to be inopportune with this e-mail, which initially was sent as private message to "maubp". I’m new novice in the world of NGS data sets analysis. I've reading many posts (samtools, seqanswers) about the different few ways that exist to process back SAM/BAM files into the fastq format that the aligners expect. According to my search, I think many of you have posted different suggestions about the challenges that this represents and what we should consider if we plan to perform this action.
Due that this messages were posted about two years ago, some of them older. See links:
As the amount of post is really diverse, and sometimes contradictory among some members, I would appreciate if you could help me to figure out if there are new ways to perform this action to recover the all relevant information, reads IDs and also keep the orphans to be considered as part of the new FASTQ files. If not, could you help me to clarify how can I proceed with this step by step?
I do really need to perform new alignments with the new genome references that have been released recently, but also others that we have generated. Unfortunately for me, I just had access to the bam files obtained from pair ended reeds that were friendly provided by other research groups.
Please apologise me if due to my unfamiliarity, I missed some clue or basic points from previous posts. I also sorry for the long message!!
Many many thanks,
Best regards,
Varo
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