Hello, I wish to convert a bam file to a fastq file. However using Picard's Sam2Fastq, I lost around 19% of the reads:
Using the command: samtools flagstat 5842_7#1.bam I found that my bam file had 57917111 paired reads. Running the command: java -Xmx4g -jar SamToFastq.jar I=5842_7#1.bam F=5842_7#1.end1.fq F2=5842_7#1.end2.fq FU=5842_7#1.unpaired.fq left me with a the end1.fq and end2.fq with 46859131 reads each (and the unpaired.fq file empty). Initially I thought that pass filtering may have thrown out the low quality reads, but using the option to include them: java -Xmx4g -jar SamToFastq.jar I=5842_7#1.bam F=5842_7#1.end1.fq F2=5842_7#1.end2.fq FU=5842_7#1.unpaired.fq INCLUDE_NON_PF_READS=true still results in the same number of reads. Does anyone know why this happens and if there is a way around this? I have resorted to using BEDTools, which is roughly three times slower than Picard, but does keep all the reads. Thank you in advance for any help, Justin ------------------------------------------------------------------------------ Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
