Question: Samtools Rmdup, file output empty
0
gravatar for mmukhame321
4.4 years ago by
mmukhame32130
United States
mmukhame32130 wrote:

Hello, 

I am trying to output a file that removed PCR duplicates by using rmdup command. My file is single-ends.

I put this into my terminal: samtools rdup [-s] input path file directory > output path file and file name.bam

 

It makes the file, the only thing is that the file is empty. Any ideas why?

 

Thanks.

ADD COMMENTlink modified 4.4 years ago by Nicola Casiraghi450 • written 4.4 years ago by mmukhame32130
1

Are you using this command?

samtools rmdup -s input.bam output.bam

You don't need '>' symbol to get the output bam.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by iraun3.6k

">" explains empty output.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Nicola Casiraghi450
1

Exactly :-)

ADD REPLYlink written 4.4 years ago by iraun3.6k

Thank you! I overlooked that, and got the results I needed! 

 

 

ADD REPLYlink written 4.4 years ago by mmukhame32130
0
gravatar for Nicola Casiraghi
4.4 years ago by
Germany, Heidelberg, DKFZ EMBL
Nicola Casiraghi450 wrote:
samtools rmdup -s input.bam out.bam

input.bam must be sorted (samtools sort).

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Nicola Casiraghi450
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