BAM to SAM tool no way to get an unsorted SAM?

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BAM to SAM tool no way to get an unsorted SAM?

Alistair Chilcott
Hello all,

My users are trying to use a tool called bismark and it requires an unsorted SAM file for one of its steps

Previous steps produce BAM files so we would like to include the tool BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort by default and there is no way to alter this behaviour.

Is there another tool that would convert a BAM to a SAM without sorting it or can the BAM-to-SAM tool be altered to include a checkbox for an unsorted result?


Regards,

Alistair


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Re: BAM to SAM tool no way to get an unsorted SAM?

Peter Cock
Do you mean a SAM/BAM file sorted by read name?
If so, try samtools sort -n ... instead.

Peter

On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott
<[hidden email]> wrote:

> Hello all,
>
> My users are trying to use a tool called bismark and it requires an unsorted SAM file for one of its steps
>
> Previous steps produce BAM files so we would like to include the tool BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort by default and there is no way to alter this behaviour.
>
> Is there another tool that would convert a BAM to a SAM without sorting it or can the BAM-to-SAM tool be altered to include a checkbox for an unsorted result?
>
>
> Regards,
>
> Alistair
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: BAM to SAM tool no way to get an unsorted SAM?

Alistair Chilcott
I guess that is my point .. at a command prompt that can be achieved ( and gives the result they need ) but as far as I can see the same is not true via the Galaxy GUI ( unless there is a tool I am missing)

They have 96 separate files to process hence the desire to use a workflow.

Regards,

Alistair




-----Original Message-----
From: Peter Cock [mailto:[hidden email]]
Sent: Thursday, 28 August 2014 2:27 PM
To: Alistair Chilcott
Cc: [hidden email]
Subject: Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM?

Do you mean a SAM/BAM file sorted by read name?
If so, try samtools sort -n ... instead.

Peter

On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott <[hidden email]> wrote:

> Hello all,
>
> My users are trying to use a tool called bismark and it requires an
> unsorted SAM file for one of its steps
>
> Previous steps produce BAM files so we would like to include the tool BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort by default and there is no way to alter this behaviour.
>
> Is there another tool that would convert a BAM to a SAM without sorting it or can the BAM-to-SAM tool be altered to include a checkbox for an unsorted result?
>
>
> Regards,
>
> Alistair
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this and other
> Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: BAM to SAM tool no way to get an unsorted SAM?

Peter Cock
Ah - I missed this was on the Galaxy list, sorry.

I think that Galaxy automatically coordinate sorts "bam" files,
which is generally a good thing bar cases like yours. This
problem has undoubtedly come up before - an "unsortedbam"
datatype may be needed...

Peter

On Thu, Aug 28, 2014 at 1:35 PM, Alistair Chilcott
<[hidden email]> wrote:

> I guess that is my point .. at a command prompt that can be
> achieved ( and gives the result they need ) but as far as I can
> see the same is not true via the Galaxy GUI ( unless there is
> a tool I am missing)
>
> They have 96 separate files to process hence the desire to use a workflow.
>
> Regards,
>
> Alistair
>
>
>
>
> -----Original Message-----
> From: Peter Cock [mailto:[hidden email]]
> Sent: Thursday, 28 August 2014 2:27 PM
> To: Alistair Chilcott
> Cc: [hidden email]
> Subject: Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM?
>
> Do you mean a SAM/BAM file sorted by read name?
> If so, try samtools sort -n ... instead.
>
> Peter
>
> On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott <[hidden email]> wrote:
>> Hello all,
>>
>> My users are trying to use a tool called bismark and it requires an
>> unsorted SAM file for one of its steps
>>
>> Previous steps produce BAM files so we would like to include the tool BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort by default and there is no way to alter this behaviour.
>>
>> Is there another tool that would convert a BAM to a SAM without sorting it or can the BAM-to-SAM tool be altered to include a checkbox for an unsorted result?
>>
>>
>> Regards,
>>
>> Alistair
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this and other
>> Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: BAM to SAM tool no way to get an unsorted SAM?

Alistair Chilcott
In reply to this post by Alistair Chilcott
As feedback to the list ....

I have solved my problem below and a number of other issues I have had since then with the "Toolfactory" available now from the Main Tool Shed (shameless plug) that was created Ross Lazarus et al.

This tool allowed me to create a tool that was exactly what I wanted (a small scriptlet for R, perl, python, or bash)
The process was straight forward, and Ross was also very helpful. Thanks also to John Chilton who helped to add an output option that I needed.
http://www.ncbi.nlm.nih.gov/pubmed/23024011

https://www.youtube.com/watch?v=Nzzc9zHZJjE

https://wiki.galaxyproject.org/DevNewsBriefs/2012_09_20#Galaxy_Tool_Factory

Please be sure and heed the warning about NOT installing it on production Galaxy servers though.

Regards,

Alistair

(p.s. I have no affiliation with the creators of the Toolfactory, but I did find it useful, YMMV)


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Alistair Chilcott
Sent: Thursday, 28 August 2014 2:36 PM
To: Peter Cock
Cc: [hidden email]
Subject: Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM?

I guess that is my point .. at a command prompt that can be achieved ( and gives the result they need ) but as far as I can see the same is not true via the Galaxy GUI ( unless there is a tool I am missing)

They have 96 separate files to process hence the desire to use a workflow.

Regards,

Alistair




-----Original Message-----
From: Peter Cock [mailto:[hidden email]]
Sent: Thursday, 28 August 2014 2:27 PM
To: Alistair Chilcott
Cc: [hidden email]
Subject: Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM?

Do you mean a SAM/BAM file sorted by read name?
If so, try samtools sort -n ... instead.

Peter

On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott <[hidden email]> wrote:

> Hello all,
>
> My users are trying to use a tool called bismark and it requires an
> unsorted SAM file for one of its steps
>
> Previous steps produce BAM files so we would like to include the tool BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort by default and there is no way to alter this behaviour.
>
> Is there another tool that would convert a BAM to a SAM without sorting it or can the BAM-to-SAM tool be altered to include a checkbox for an unsorted result?
>
>
> Regards,
>
> Alistair
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this and other
> Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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