Hi,
I need to assembly some unmapped reads from Tophat2's output "unmapped.bam"
Firstly I have to extract read pairs from unmapped.bam
I found two tools for it:
and
results:
bedtools_un1.fastq has 685 MB
picard_un1.fastq has 915 MB
My question is, why the difference in the size of files is so big?
Shouldn't the result files be the same? (as the inmput "unmapped.bam" is the same)
I need to assembly some unmapped reads from Tophat2's output "unmapped.bam"
Firstly I have to extract read pairs from unmapped.bam
I found two tools for it:
Code:
bedtools bamtofastq -i unmapped.bam -fq bedtools_un1.fastq -fq2 bedtools_un2.fastq
Code:
java -jar SamToFastq.jar I=unmapped.bam F=picard_un1.fastq F2=picard_un2.fastq VALIDATION_STRINGENCY=SILENT
bedtools_un1.fastq has 685 MB
picard_un1.fastq has 915 MB
My question is, why the difference in the size of files is so big?
Shouldn't the result files be the same? (as the inmput "unmapped.bam" is the same)
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