Kallisto - Revision history

Rf at 11:55, 9 June 2016

2016-06-09T11:55:28Z

2016-05-26T22:24:20Z

2016-05-26T22:23:01Z

2016-05-26T21:29:48Z

2016-05-26T21:25:15Z

2016-05-26T16:47:42Z

2016-05-26T16:38:16Z

2016-05-26T16:25:13Z

2016-05-26T16:11:43Z

2016-05-26T13:31:10Z

@@ Line 61: / Line 61: @@
 Sleuth is an associated program for Kallisto, when dealing with several samples for which we have pair-end read sets. It is implemented in R and is available in Bioconductor.
-If already installed, it can be loaded, like all other R modules, it - and its dependencies - are loaded as follows:
+It is installed on R/3.2.1. modules (which all users have loaded up by default). To activiate once inside the R interpreter, like all other R modules:
   library(sleuth)
- source("http://bioconductor.org/biocLite.R")
+Sleuth is made up of the various programs (only a few show here, please see manual in links section):
 * '''sleuth_prep''', preparation stage.
@@ Line 80: / Line 75: @@
 see links for more details
-== Links ==
+= Links =
 * Kallisto's own getting started page at [https://pachterlab.github.io/kallisto/starting.html starting]
 * [http://pachterlab.github.io/sleuth/manual sleuth manual]
@@ Line 86: / Line 82: @@
 * [https://benchtobioinformatics.wordpress.com/2015/07/10/using-kallisto-for-gene-expression-analysis-of-published-rnaseq-data benchtobioinformatics]
 * [http://andrewtmckenzie.com/2015/05/12/how-to-run-kallisto-on-ncbi-sra-rna-seq-data-for-differential-expression-using-the-mac-terminal Andrew MacKenzie]

@@ Line 55: / Line 55: @@
 * we are running 4 bootstraps here ('''-b 4''')
 * each sample is launch in parallel in a separate kallisto instance. Beyond that the bootstrap can also be parallelised with the '''-t 4''' option.
 = Sleuth =

@@ Line 29: / Line 29: @@
 However, for cluster usage, and for more than a few samples, it is best to use a job script, and specifically, the job-array mode of Gridengine, the queue manager. First the sample filenames should be listed out in a text file, one pair per line. For example, like so:
-The following qsub command line launches the jobscript in the job array mode, which basically launches the job script N time sin parallel, where here N will equal the number of lines (i.e. number of paired reads). This mode allocates a ${SGE_TASK_ID} variable to each of the parallel script and these can be used internally within the script to represent a certain member of the paired read listing file.
+ ls *_{1,2}.{fastq,fastq.gz} >listingfile.txt
 And here is the related jobscript:
   #!/bin/bash
@@ Line 46: / Line 51: @@
   II=$(($I+1))
   kallisto quant -i trinity_out_dir/gryllemb_trin.idx -b $NSLOTS --plaintext -t $NSLOTS -o out_${SGE_TASK_ID} ${A[$I]} ${A[$II]}
 = Sleuth =

@@ Line 29: / Line 29: @@
 However, for cluster usage, and for more than a few samples, it is best to use a job script, and specifically, the job-array mode of Gridengine, the queue manager. First the sample filenames should be listed out in a text file, one pair per line. For example, like so:
 And here is the related jobscript:
   #!/bin/bash

@@ Line 29: / Line 29: @@
 However, for cluster usage, and for more than a few samples, it is best to use a job script, and specifically, the job-array mode of Gridengine, the queue manager. First the sample filenames should be listed out in a text file, one pair per line. For example, like so:
+And here is the related jobscript:
 = Sleuth =

@@ Line 17: / Line 17: @@
 * the reference or assembly follows with no associated option
-Armed with the index file, kallisto is now ready to quantify. Here is the format of the command:
+Armed with the index file, kallisto is now ready to quantify. Here is the basic format of the command:
   kallisto quant -i <index_file> -o outputdir <one_pair_of_read_files>
-wih severalFor cluster usgae
+wih several
-<ins>Explanation<ins>:
+<ins>Explanation</ins>:
 * Kallisto only takes one sample at a time, which most often will mean one pair of fastq files. If the sample is spread over several pairs of files, they can all follow each other n the command line. This might make it look that kallisto takes more than one sample, but that's wrong. In summary: one sample only to kallisto. The integration of the different samples into the analysis appears to be the job of sleuth.
 = Sleuth =

← Older revision		Revision as of 16:25, 26 May 2016
Line 49:		Line 49:
	* [https://benchtobioinformatics.wordpress.com/2015/07/10/using-kallisto-for-gene-expression-analysis-of-published-rnaseq-data benchtobioinformatics]		* [https://benchtobioinformatics.wordpress.com/2015/07/10/using-kallisto-for-gene-expression-analysis-of-published-rnaseq-data benchtobioinformatics]
	* [http://andrewtmckenzie.com/2015/05/12/how-to-run-kallisto-on-ncbi-sra-rna-seq-data-for-differential-expression-using-the-mac-terminal Andrew MacKenzie]		* [http://andrewtmckenzie.com/2015/05/12/how-to-run-kallisto-on-ncbi-sra-rna-seq-data-for-differential-expression-using-the-mac-terminal Andrew MacKenzie]
−
−	~~=Analysis=~~
−
−	~~Also part of Lior Pachter's lab is the Sleuth software and this is recommended for analysis of kallisto output~~

@@ Line 19: / Line 19: @@
 Armed with the index file, kallisto is now ready to quantify. Here is the format of the command:
-  kallisto quant -i <index_file> -o outputdir <then_follow_read_pair_file>
+  kallisto quant -i <index_file> -o outputdir <then_follow_read_pair_files>
 = Sleuth =