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Old 02-27-2014, 02:59 AM   #1
reema
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Talking Picard SamToFastq strange behavious

Dear all,

I am using picard SamtoFastq in oredr to convert BAM/SAM to fastq. I have a paired end sample. I am using following command:-

java -jar SamToFastq.jar INPUT=input.bam FASTQ=input_1.fastq SECOND_END_FASTQ=input_2.fastq VALIDATION_STRINGENCY=LENIENT

The command runs without error and generate two file. Now the problem is input_1.fastq has all the reads where as input_2.fastq is empty(o byte file). I have no idea why it's happening. I tried following option but no luck,
1) Sorted bam -> SamToFastq
2) BAM to SAM -> SamToFastq

Any suggestion would be very helpful.

Thanks,
Reema SIngh
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Old 02-27-2014, 06:32 AM   #2
TiborNagy
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Maybe you BAM file is not a paired end sample. Check it manually.
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Old 03-05-2014, 07:27 AM   #3
reema
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Quote:
Originally Posted by TiborNagy View Post
Maybe you BAM file is not a paired end sample. Check it manually.
Thanks TiborNagy,

You are right,my file is not paired..
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