Samtools Rmdup, file output empty
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
• 4,346 views
•
link
updated
by
Ram
•
written
by
mmukhame321 •
•
written
by
mmukhame321 •
1 answer
samtools rmdup -s input.bam out.bam
input.bam must be sorted (samtools sort).
• 0 views
•
link
updated
by
Ram
•
written
by
Nicola Casiraghi
•
written
by
Nicola Casiraghi
Log in to answer this question.
More posts like this
-
How to properly pass from samtools rmdup to samtools markdup
written by raggi.emanuele •
-
samtools markdup vs samtools rmdup
written by a.abnousi •
-
samtools mpileup keeps making an empty file
written by James Reeve
-
Removing Duplicates before aligning
written by newbinf •
-
Picard vs samtools rmdup
written by xd_d
-
Samtools: removing PCR duplicates
written by devinliao0918 •
-
Remove Duplicates Workflow
written by Anjan
-
Samtools And Flagstat
written by nbvasani
-
Subsampling Bam File With Samtools
written by madbessoul •
-
Removing Pcr Duplicates From Bam Without Collapsing Sequences By Position?
written by user
Are you using this command?
You don't need '
>' symbol to get the output bam.>explains empty output.Exactly :-)
Thank you! I overlooked that, and got the results I needed!