Hi all,
I downloaded the Denisova BAM file from here.
Since this file is aligned to the 1000 genomes reference genome and I would like to align it to grch38 I started the following utility for BAM to FASTQ conversion http://gsl.hudsonalpha.org/information/software/bam2fastq
After the file converted the FASTQ file is about 180GB whereas the BAM file is 80GB.
My question is does this seem correct and is there a way to estimate the size of FASTQ from a BAM file?
If there is faster converter please could you share, thanks in advance.
BAM files are compressed, the fastq file that that outputs isn't, so yes, that's not unreasonable. Given the notice at the top of the bam2fastq page, I wouldn't be surprised if Picard is faster. It might also allow writing compressed files (no clue, I've never used its SamToFastq command).
FYI: SamToFastq
(...) COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and GELI). Default value:5.
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written
by
Pierre Lindenbaum
You saved me from looking at the documentation :)
I edited your post to make it a bit more correct. Note that if paired-end reads are being used here that that won't work (and don't forget orphaned reads...).
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written
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Devon Ryan
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