The two tools have different reporting options on the tool forms. Perhaps these were not set in a way that would produce the same output?
For reference, the most current tool versions in Galaxy:
BEDTools >> Convert from BAM to FastQ (Galaxy Version 126.96.36.199)
Picard >> SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq (Galaxy Version 188.8.131.52)
Thanks! Jen, Galaxy team
hi Jen thanks for the answer.
I've used the bedtools bamtofastq on a bam generated by galaxy then I use the galaxy tool.
so the input is the same, but these are the sizes: bedtools: read1 28679667 read2 28767491
galaxy read1 72646227 read2 83312211
i ran the bedtools bamtofastq from the command line and I also got this warning message: "*WARNING: Query HS38_18980:1:1116:9578:21925 is marked as paired, but it's mate does not occur next to it in your BAM file. Skipping."
can the difference in size accout for the fact that bedtools is excluding unmated reads?