Paired end reads are not supported in rmdup.py

[adriaan-vd-graaf]

Dear Sir,

The script rmdup.py only supports single end reads, while this is not stated anywhere. It may nice to have this functionality implemented, or at least a warning about this in the documentation.

Thank you for your time,
Adriaan

[machadoheather]

I would also be interested in rmdup.py functionality for paired end reads. Is that in the works, by any chance?

Best,
Heather

[bmvdgeijn]

Hi Adriaan and Heather,

We will work on adding that functionality in now. Our apologies for the
delay, we have been swamped by revisions.

On Mon, Jun 8, 2015 at 8:35 PM, machadoheather notifications@github.com
wrote:

I would also be interested in rmdup.py functionality for paired end reads.
Is that in the works, by any chance?

Best,
Heather

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Reply to this email directly or view it on GitHub
#5 (comment).

[bmvdgeijn]

We added a script for paired end rmdup. It currently assumes that the
pairs can be matched based on query name (the first column of the bam
files) and that the input is sorted.

On Thu, Mar 19, 2015 at 6:21 AM, adriaan-vd-graaf notifications@github.com
wrote:

Dear Sir,

The script rmdup.py only supports single end reads, while this is not
stated anywhere. It may nice to have this functionality implemented, or at
least a warning about this in the documentation.

Thank you for your time,
Adriaan

—
Reply to this email directly or view it on GitHub
#5.

[machadoheather]

Wonderful, thank you!

Best,
Heather

On Wed, Jul 1, 2015 at 3:22 PM, Bryce van de Geijn <notifications@github.com

wrote:

We added a script for paired end rmdup. It currently assumes that the
pairs can be matched based on query name (the first column of the bam
files) and that the input is sorted.

On Thu, Mar 19, 2015 at 6:21 AM, adriaan-vd-graaf <
notifications@github.com>
wrote:

Dear Sir,

The script rmdup.py only supports single end reads, while this is not
stated anywhere. It may nice to have this functionality implemented, or
at
least a warning about this in the documentation.

Thank you for your time,
Adriaan

—
Reply to this email directly or view it on GitHub
#5.

—
Reply to this email directly or view it on GitHub
#5 (comment).