This is a test version of Biostars. For the public version, visit https://www.biostars.org.
unmapped reads BAM TCGA

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
• 2,021 views • link
updated by GenoMax GenoMax • written by Taktak31 • Taktak31

2 answers

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

• 0 views • link
written by GenoMax GenoMax

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

• 0 views • link
written by Taktak31 • Taktak31

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

• 0 views • link
written by GenoMax GenoMax
  • 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.
• 0 views • link
written by pbpanigrahi pbpanigrahi

Log in to answer this question.

More posts like this