unmapped reads BAM TCGA

Question

[Taktak31]

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?

Answer 1

[GenoMax]

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

[Taktak31]

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

[GenoMax]

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

Answer 2

[pbpanigrahi]

• 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.