Differences of reads between uBam and fastq from Ion Torrent
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2.7 years ago

I'm sorry for the naive question, but could someone explain to me, the differences of reads in Ion Torrent, between the uBAM format and FASTQ? Shouldn't the number of reads be the same?

alignment sequencing • 1.2k views
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Hi ,

Yes it's the same number as fastq. They choose this format because it's saving space because it's compressed format et fastq is not. The u of uBam mean unaligned.

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Thats the issue, the report generated with uBAM gave me a different number of reads comparing to the FASTQ files.

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Perhaps the fastq files are filtered (for quality or something else)?

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@genomax explanation is certainly rigth. You should confirme this by checking the torrent suite documentation if you are using it ( i told you that because in my version we add a fastq = to uBam in termes of reads, so low quality reads where removes from the fastq).

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