Converting bam to fastq filee/bam2fastx error

[bob-loblaw]

Hi all,

I'm getting the following error when I try to use bam2fastx on tophat unmapped.bam output

Error: couldn't retrieve both reads for pair x

(where x is the sequence ID)

Since my data is paired ends I gave it the -P parameter. I'm assuming that bam2fastx requires pairs to be next to each other in the file, and then it just writes them both out to a fasta/fastq file. But I've tried sorting the bam file using samtools sort -n and I'm still getting the same problem (albeit with a different sequence ID). As far as I can see there shouldn't be any sequences in the unmapped.bam file which do not have a pair as the programs I've used to process them so far all take paired end files as input, and output 2 PE files. Could anyone offer some advice? I've looked into using picards SamToFastq but my files are very large and SamToFastq keeps failing because of memory errors. I also thinking maybe it's just a handful of reads giving this problem which don't have a pair in the data, does anyone know how to remove a specified read from a bam/sam file?

Thanks