question about SRMA

rlh · 10-21-2010, 06:33 PM

i am a freshman in this field, i am trying to use SRMA to realign my data, but i don't know how to generate a ranges file for SRMA, it is a txt file, the content is like:
chr1 1889866 1890066
chr1 12561395 12561595
chr1 34999494 34999694
chr1 43681831 43682031
chr1 74810345 74810545
chr1 74810352 74810552
chr1 89245929 89246129
chr1 143585219 143585419
chr1 144037256 144037456
chr1 150462252 150462452
chr1 156418029 156418229
chr1 169823406 169823606
chr1 227839825 227840025

any body any suggest?i will appreciate your help!

nilshomer · 10-21-2010, 07:18 PM

Quote:

Originally Posted by rlh

i am a freshman in this field, i am trying to use SRMA to realign my data, but i don't know how to generate a ranges file for SRMA, it is a txt file, the content is like:
chr1 1889866 1890066
chr1 12561395 12561595
chr1 34999494 34999694
chr1 43681831 43682031
chr1 74810345 74810545
chr1 74810352 74810552
chr1 89245929 89246129
chr1 143585219 143585419
chr1 144037256 144037456
chr1 150462252 150462452
chr1 156418029 156418229
chr1 169823406 169823606
chr1 227839825 227840025

any body any suggest?i will appreciate your help!

That looks fine, what was the error?

rlh · 10-21-2010, 07:39 PM

Quote:

Originally Posted by nilshomer

That looks fine, what was the error?

perhaps i didn't say clearly, i just wanna know how to generate that RANGES file. can you offer some advices?

nilshomer · 10-21-2010, 07:49 PM

Oh, well if you have regions that you are interested in, use a ranges file. Otherwise, you can run it without the ranges file, which will re-align your entire dataset.

rlh · 10-21-2010, 08:07 PM

Quote:

Originally Posted by nilshomer

Oh, well if you have regions that you are interested in, use a ranges file. Otherwise, you can run it without the ranges file, which will re-align your entire dataset.

thankyou for your reply! my database is 56G, if i run re-align in the entire database, the memory it needs is extreme, so i wanna run it with RANGES file.
is there any tools can help me generate RANGES file from my database, if i write it by myself will cost such a long time.

nilshomer · 10-21-2010, 08:09 PM

Quote:

Originally Posted by rlh

thankyou for your reply! my database is 56G, if i run re-align in the entire database, the memory it needs is extreme, so i wanna run it with RANGES file.
is there any tools can help me generate RANGES file from my database, if i write it by myself will cost such a long time.

It doesn't load the entire reference and reads into memory, it loads them in as needed. I assume by database, you mean reference.

rlh · 10-21-2010, 08:30 PM

Quote:

Originally Posted by nilshomer

It doesn't load the entire reference and reads into memory, it loads them in as needed. I assume by database, you mean reference.

i run a 5G testing data, 64* coverage, -Xmx8G, it print "Error: java heap space", and the records processing stop at about 11000000, someone suggest me to do it with RANGES file.

krobison · 10-22-2010, 06:05 AM

A Nils (who wrote the program, so he might understand it :-) said, if you want to speed things up you can use the ranges file to specify specific regions of interest. You, and only you, can decide what you find interesting.

Probably you want to pick a bunch of genes of interest & then extract the columns for them from the annotation file off UCSC for the genome you are interested in. That's pretty trivial with Perl/Python/Java/whathaveyou (or even with grep & cut in UNIX) & the time you invest now to learn how to do it will pay off many times over.

rlh · 10-22-2010, 07:06 AM

Quote:

Originally Posted by krobison

A Nils (who wrote the program, so he might understand it :-) said, if you want to speed things up you can use the ranges file to specify specific regions of interest. You, and only you, can decide what you find interesting.

Probably you want to pick a bunch of genes of interest & then extract the columns for them from the annotation file off UCSC for the genome you are interested in. That's pretty trivial with Perl/Python/Java/whathaveyou (or even with grep & cut in UNIX) & the time you invest now to learn how to do it will pay off many times over.

thank you! i understand it now, i am really appreciate!

rlh · 10-22-2010, 07:08 AM

i understand what you mean now. thanks very much!

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10-21-2010, 06:33 PM	#1
rlh Member Location: China Join Date: Oct 2010 Posts: 12	question about SRMA i am a freshman in this field, i am trying to use SRMA to realign my data, but i don't know how to generate a ranges file for SRMA, it is a txt file, the content is like: chr1 1889866 1890066 chr1 12561395 12561595 chr1 34999494 34999694 chr1 43681831 43682031 chr1 74810345 74810545 chr1 74810352 74810552 chr1 89245929 89246129 chr1 143585219 143585419 chr1 144037256 144037456 chr1 150462252 150462452 chr1 156418029 156418229 chr1 169823406 169823606 chr1 227839825 227840025 any body any suggest?i will appreciate your help!

10-21-2010, 07:49 PM	#4
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	Oh, well if you have regions that you are interested in, use a ranges file. Otherwise, you can run it without the ranges file, which will re-align your entire dataset.

10-22-2010, 06:05 AM	#8
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	A Nils (who wrote the program, so he might understand it :-) said, if you want to speed things up you can use the ranges file to specify specific regions of interest. You, and only you, can decide what you find interesting. Probably you want to pick a bunch of genes of interest & then extract the columns for them from the annotation file off UCSC for the genome you are interested in. That's pretty trivial with Perl/Python/Java/whathaveyou (or even with grep & cut in UNIX) & the time you invest now to learn how to do it will pay off many times over.

10-22-2010, 07:08 AM	#10
rlh Member Location: China Join Date: Oct 2010 Posts: 12	i understand what you mean now. thanks very much!