SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
bfast postprocess "AlignedEntryGetAlignment" error sdvie Bioinformatics 4 03-02-2016 09:13 AM
Bowtie with -p argument RNA-seq Bioinformatics 0 05-25-2011 05:30 PM
BFAST memory error in postprocess Marisa_Miller Bioinformatics 3 09-18-2010 04:35 AM
bfast postprocess -U option dmurdock Bioinformatics 9 04-22-2010 12:22 PM
bfast postprocess error m_elena_bioinfo Bioinformatics 0 11-11-2009 08:45 AM

Reply
 
Thread Tools
Old 08-08-2011, 07:17 AM   #1
david.tamborero
Member
 
Location: spain

Join Date: Feb 2011
Posts: 60
Default -r argument from Bfast postprocess

I'm not sure of the use of the -r argument in the Bfast postprocess command. Can somebody who used it give an example of the required input file? I'm getting parse errors in all my attempts...

Thank you very much!
David
david.tamborero is offline   Reply With Quote
Old 08-08-2011, 11:22 AM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

The line in the file should match exactly to what you would expect in the output of a SAM file. So that includes the tab separated fields, etc. Please post the contents of your input file.
nilshomer is offline   Reply With Quote
Old 08-09-2011, 02:14 AM   #3
david.tamborero
Member
 
Location: spain

Join Date: Feb 2011
Posts: 60
Default

I've created a text file containing the following entry:

Code:
@RG   readgroups_name
and also:

Code:
@RG   RG:readgroups_name
(both tab-separated)

and I get the following error:

Code:
In function "ParseReadGroup": Fatal Error[OutOfRange]. Variable/Value: readGroupString.
Message: Could not parse read group.
 ***** Exiting due to errors *****
david.tamborero is offline   Reply With Quote
Old 08-09-2011, 06:55 AM   #4
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Look at the SAM spec. What tags are required for the RG field (Hint: there is no RG tag in the RG header section)?

Try:
Code:
@RG<tab>ID:MYID
nilshomer is offline   Reply With Quote
Old 08-10-2011, 06:44 AM   #5
david.tamborero
Member
 
Location: spain

Join Date: Feb 2011
Posts: 60
Default

ops, once again I did it wrong. It worked when I used a correct tag for the @RG entry.

Tahnks a lot!
david.tamborero is offline   Reply With Quote
Old 08-16-2012, 04:07 PM   #6
cllorens
Member
 
Location: Valencia

Join Date: Nov 2011
Posts: 44
Default

Hi Nils

I experienced the same difficulty than David and saw this thread

I tried with my sample that has for instance the ID solid_0735

then have created a RGfilename file with @RG ID:solid0735_hg19.1 and worked, good!

but now i wonder if it is possible to add more info about library, sample and platform?

the manual says that you can do it with the LB but what about SM and PL

according to the sintaxis indicated above i created a new file with the following flag

@RG ID:solid0735_hg19.1 LB:solid0735_master SM:human_muscle1 PL:solid

(it is just an example)

but it did not work (the shell says that cannot parse the file)

then i tried the following

@RG ID:solid0735_hg19.1\LB:solid0735_master\SM:human_muscle1\PL:solid

and didnt work either, perhaps (by sure) i am doing something wrong

thanks

Carlos
cllorens is offline   Reply With Quote
Old 08-18-2012, 12:28 PM   #7
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

It should work, but the only way to know is to try.
nilshomer is offline   Reply With Quote
Old 08-18-2012, 03:31 PM   #8
cllorens
Member
 
Location: Valencia

Join Date: Nov 2011
Posts: 44
Default

That is a very poor answer Nils.
As I said, I already tried and did not work.
Of course if I try again and again and again I will find the answer but I would really appreciate i you give some key to follow, maybe the tags abreviations are not appropiate I do not known. Anyway thank you for answering.
cllorens is offline   Reply With Quote
Old 08-18-2012, 03:54 PM   #9
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by cllorens View Post
That is a very poor answer Nils.
As I said, I already tried and did not work.
Of course if I try again and again and again I will find the answer but I would really appreciate i you give some key to follow, maybe the tags abreviations are not appropiate I do not known. Anyway thank you for answering.
Please try inputting it exactly as you would in a normal SAM file. The string will be written exactly as it is given. So you should include the tab characters as well. Here's what the manual says:

Code:
-r STRING, --readGroupFileName=STRING
Specifies to add the read group (@RG) line to add to the header, which is given in the specified file. Additionally, the appropriate read group (RG) tag (and LB tag if present) will be added to each read. Make sure that the line is exactly the same as what would be printed to the SAM file, which includes the “@RG” string
nilshomer is offline   Reply With Quote
Old 08-22-2012, 04:10 PM   #10
cllorens
Member
 
Location: Valencia

Join Date: Nov 2011
Posts: 44
Default

it only works when i only use the ID tag as you note above Nils
but i am unable to make it work if I add some other tags such as LB, SM and PL
I do not know i tried with tabs with bars with inverter bars etc and with different
combinations of these three with the ID tag and in those cases always find a error
message sayind than cannot parse the RGfilename fle ID.

This one

In function "ParseReadGroup": Fatal Error[OutOfRange]. Variable/Value: readGroupString.
Message: Could not parse read group; read ID required.
***** Exiting due to errors ***


I will try again with other combinations.

It might be that any of these additional tags should be in the .baf or in the previous fastq, or .bmf files in order to work later in the sam creation step?

In principle, there is not a big problem as I can live only appending the ID tag but it would be good to known how to add the remainder. I will make more attempts anyway.

Thanks
Carlos
cllorens is offline   Reply With Quote
Old 08-22-2012, 04:48 PM   #11
cllorens
Member
 
Location: Valencia

Join Date: Nov 2011
Posts: 44
Default

Ok solved at the first subsequent attempt Nils,
it was in front my eyes and as it easier it was i did not see it.
i was putting spaces between the tags instead of tabs.
using this sintax "@RG<tab>ID:my_ID<tab>LB:my_LB<tab>SM:my_SM<tab>PL:my_PL" works.
Well, today i will be a little bit happier.
Carlos
cllorens is offline   Reply With Quote
Reply

Tags
bfast, bfast postprocess, readgroups

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:47 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO