-r argument from Bfast postprocess

[david.tamborero]

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

[nilshomer]

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.

[david.tamborero]

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

@RG   readgroups_name

and also:

@RG   RG:readgroups_name

(both tab-separated)

and I get the following error:

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

[nilshomer]

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:

@RG<tab>ID:MYID

[david.tamborero]

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

Tahnks a lot!

[cllorens]

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

[nilshomer]

It should work, but the only way to know is to try.

[cllorens]

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.

[nilshomer]

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:

-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

[cllorens]

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]

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