Thor - Revision history

Rf at 21:47, 28 June 2017

2017-06-28T21:47:31Z

Rf at 15:14, 16 June 2017

2017-06-16T15:14:36Z

Rf at 10:01, 6 June 2017

2017-06-06T10:01:10Z

Rf at 09:59, 6 June 2017

2017-06-06T09:59:52Z

Rf at 09:21, 6 June 2017

2017-06-06T09:21:40Z

Rf at 09:18, 6 June 2017

2017-06-06T09:18:34Z

Rf at 15:23, 5 June 2017

2017-06-05T15:23:20Z

Rf at 15:19, 5 June 2017

2017-06-05T15:19:09Z

Rf: Created page with "= Introduction = This is one of the newer Differential Peak callers from Costalab in Aachen. = Usage = == a first run == The first few runs are usually error-prone. Thor i..."

2017-06-05T13:33:21Z

Created page with "= Introduction = This is one of the newer Differential Peak callers from Costalab in Aachen. = Usage = == a first run == The first few runs are usually error-prone. Thor i..."

New page

= Introduction =

This is one of the newer Differential Peak callers from Costalab in Aachen.

= Usage =

== a first run ==

The first few runs are usually error-prone. Thor is no exception:

rgt-THOR first.config --report --no-correction --output-dir ./thorfirst -n THOR_DCfirst

<ins>Explanation</ins>:
* '''first.config''', this is a configuration file, see below
* '''--output-dir''', program will fail to run if this already exists.

The contents of the <code>first.config</code> is as follows:

#rep1
WTIP_S5_L001/WTIP_S5_L001_srtd.bam
WTIP_S5_L002/WTIP_S5_L002_srtd.bam
#rep2
USL1IP_S7_L001/USL1IP_S7_L001_srtd.bam
USL1IP_S7_L002/USL1IP_S7_L002_srtd.bam
#genome
/storage/home/users/as363/w303_genome/w303.fa
#chrom_sizes
/storage/home/users/as363/w303_genome/w303_.sizes
#inputs1
WTINP_S4_L001/WTINP_S4_L001_srtd.bam
WTINP_S4_L002/WTINP_S4_L002_srtd.bam
#inputs2
ULS1INP_S6_L001/ULS1INP_S6_L001_srtd.bam
ULS1INP_S6_L002/ULS1INP_S6_L002_srtd.bam

=== output from this run ===

Call DPs on whole genome.
Computing read extension sizes for ChIP-seq profiles
Compute GC-content
[fai_load] build FASTA index.
Compute factors
Normalize input of Signal 0, Rep 0 with factor 0.644
Normalize input of Signal 0, Rep 1 with factor 0.645
Normalize input of Signal 1, Rep 0 with factor 0.647
Normalize input of Signal 1, Rep 1 with factor 0.647
Use global TMM approach
TMM normalization not successfully performed, do not normalize data
TMM normalization not successfully performed, do not normalize data
TMM normalization not successfully performed, do not normalize data
TMM normalization not successfully performed, do not normalize data
Compute GC-content
Compute factors
Normalize input of Signal 0, Rep 0 with factor 0.644
Normalize input of Signal 0, Rep 1 with factor 0.645
Normalize input of Signal 1, Rep 0 with factor 0.647
Normalize input of Signal 1, Rep 1 with factor 0.647
Use global TMM approach
Compute HMM's training set
No differential peaks detected

@@ Line 230: / Line 230: @@
 This may have had something to do with a numpy update that was done between the second and third runs.
 = Links =
 * [http://www.regulatory-genomics.org/thor-2/basic-intrstruction Thor's home page]

@@ Line 192: / Line 192: @@
   Compute HMM's training set
   No differential peaks detected
 = Links =
 * [http://www.regulatory-genomics.org/thor-2/basic-intrstruction Thor's home page]

← Older revision		Revision as of 10:01, 6 June 2017
Line 135:		Line 135:

	rgt-THOR first.config --report --housekeeping-genes fourhk_yeast.bed --no-correction --output-dir ./thorsec -n THOR_DCsec		rgt-THOR first.config --report --housekeeping-genes fourhk_yeast.bed --no-correction --output-dir ./thorsec -n THOR_DCsec
		+
		+	Conifg file didn't change on this one. Out is as follows:

	Call DPs on whole genome.		Call DPs on whole genome.

@@ Line 11: / Line 11: @@
 * There is no verbose options to see what might be going wrong, though the developers are working on it.
 * There is no parallelism in this tool, it can run quite slowly. For a big sample set resercve as much as two days.
-* Neither Thor nor Odin take accoutn of paired reads in the BAM file. Recommendation from devs is to filter discordant pairs from the BAM file.
+* Neither Thor nor Odin take account of paired reads in the BAM file. Recommendation from devs is to filter discordant pairs from the BAM file.
 == Housekeeping genes ==
@@ Line 131: / Line 131: @@
   Compute HMM's training set
   No differential peaks detected

@@ Line 6: / Line 6: @@
 * [https://groups.google.com/forum/#!categories/rgtusers/odinthor https://groups.google.com/forum/#!categories/rgtusers/odinthor]
 <ins>Notes</ins>:
-* It follows on the ODIN tool which is largely supersedes.
+* Thor follows on the ODIN tool which is largely supersedes.
 * For normalization it can use the TMM method widelused in RNA-Seq (EdgeR) or a bed-format list of housekeeping genes.
 == Housekeeping genes ==
@@ Line 69: / Line 70: @@
   Normalize input of Signal 1, Rep 1 with factor 0.647
   Use global TMM approach
   Compute HMM's training set
   No differential peaks detected

@@ Line 16: / Line 16: @@
 The rationale for this approach is that they are genes that have a stable expression pattern, and so can be used to normalise all the others that don't.
 = Usage =
 == a first run ==

@@ Line 1: / Line 1: @@
 = Introduction =
-This is one of the newer Differential Peak callers from Costalab in Aachen.
+This is one of the newer Differential Peak Callers from Costalab in Aachen.
 = Usage =