unmapped reads BAM TCGA
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3 months ago
Taktak31 • 0

Hello,

on the TCGA website it says some BAM files may not have the unmapped reads available, how can I figure which BAM files may not have this? Also would I need to convert BAM to FASTQ to access the unmapped reads? If I need to convert to FASTQ, isn't it better to use the FASTQ files available on the TCGA Legacy Archive?

unmapped BAM read TCGA • 359 views
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3 months ago
GenoMax 107k

If you need fastq files then you should indeed use fastq files available at Legacy archive.

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Many studies convert the BAM files (from the harmonized TCGA dataset) to FASTQ so I was wondering why this was the case?

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Possibly because they don't care about unmapped reads and can just get the reads they want in this way?

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3 months ago
pbpanigrahi ▴ 410
  • Better to use Fastq files directly if u want fastq files instead of converting back from bam files
  • We can use samtools flagstat in.bam to get information about total reads, how many of them are mapped. This way you can figure out which bam has unmapped reads.
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