Detonate - Revision history

Rf at 14:57, 30 January 2017

2017-01-30T14:57:19Z

2017-01-30T14:57:03Z

2017-01-30T14:48:20Z

2017-01-30T14:47:41Z

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@@ Line 24: / Line 24: @@
 *# ref-eval-estimate-true-assembly
-== Usage ==
+= Usage =
 The detonate module must be loaded beforehand

← Older revision		Revision as of 14:57, 30 January 2017
Line 72:		Line 72:

	=Links=		=Links=
−	[http://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0553-5 ~~The~~ published paper describing Detonate]	+	* The [http://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0553-5 published paper] describing Detonate.
		+	* [https://github.com/deweylab/detonate source code webpage] with some usage instructions

@@ Line 53: / Line 53: @@
 * -p 8, this refers to the number of threads the program run will use. In this case 8.
 * --transcript-length-parameters, a filename contianing the output of the previous '''rsem-eval-estimate-transcript-length-distribution''' command.
-* The next option is a comma separated list of the raw reads used to assemble the de-novo transcriptome in the first place. It's probably best to build a list of these files beforehand, and pass them as a subprocess with<pre>&#10;$(cat fq.lst |tr '\n' ',')
+* The next option is a comma separated list of the raw reads used to assemble the de-novo transcriptome in the first place. It's probably best to build a list of these files beforehand, and pass them as a subprocess with<pre>&#10;$(cat fq.lst |tr '\n' ',')</pre>
 * the next option sis hte de-novo assembled fasta file

@@ Line 54: / Line 54: @@
 * --transcript-length-parameters, a filename contianing the output of the previous '''rsem-eval-estimate-transcript-length-distribution''' command.
 * The next option is a comma separated list of the raw reads used to assemble the de-novo transcriptome in the first place. It's probably best to build a list of these files beforehand, and pass them as a subprocess with<pre>&#10;$(cat fq.lst |tr '\n' ',')
 * the next option sis hte de-novo assembled fasta file
 * the penultimate option in this example is the output prefix, a name (of the users choice) which will be used to prefix the output files.

@@ Line 55: / Line 55: @@
 * The next option is a comma separated list of the raw reads used to assemble the de-novo transcriptome in the first place. It's probably best to build a list of these files beforehand, and pass them as a subprocess with<pre>&#10;$(cat fq.lst |tr '\n' ',')
 * the next option sis hte de-novo assembled fasta file
-* the penultimate option in thsi example is the output prefix, a anme of the users choice which will be used to prefix the output files.
+* the penultimate option in this example is the output prefix, a name (of the users choice) which will be used to prefix the output files.
 * the final option is a number representing the length of the raw reads.

@@ Line 53: / Line 53: @@
 * -p 8, this refers to the number of threads the program run will use. In this case 8.
 * --transcript-length-parameters, a filename contianing the output of the previous '''rsem-eval-estimate-transcript-length-distribution''' command.
-* The next option is a comma seperated list of the raw reads used to assemble the de-novo transcriptome in the first place.
+* The next option is a comma separated list of the raw reads used to assemble the de-novo transcriptome in the first place. It's probably best to build a list of these files beforehand, and pass them as a subprocess with<pre>&#10;$(cat fq.lst |tr '\n' ',')
 It's best to wrap this command in a job submission script as follows:
@@ Line 64: / Line 67: @@
   #$ -q highmemory.q
   #$ -pe multi 8
   rsem-eval-calculate-score -p $NSLOTS --transcript-length-parameters outputld.txt $(cat fq.lst |tr '\n' ',') <denovoassemblyname.fa> <output_prefix> <length_of_short_reads>
 =Links=
 [http://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0553-5 The published paper describing Detonate]

@@ Line 48: / Line 48: @@
   rsem-eval-calculate-score -p 8 --transcript-length-parameters human.txt /data/reads.fq assembly1.fa assembly1_rsem_eval 76
 =Links=
 [http://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0553-5 The published paper describing Detonate]