Dev #4

renewiegandt · 2018-12-14T15:50:29Z

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…n of all scores in this footprint

… of first and last positions with max score

… footprints.bed

…es within a peak

…t nice for the user

…lab/masterJLU2018 into motif_estiamtion

…in a window (not working yet)

…lides not, i don't know why

…2018 into dev

…o lowercase.

…2018 into dev

renewiegandt and others added 30 commits October 29, 2018 09:33

convert BED file to FASTA (one per cluster)

89eb998

removing redundant code

4c86efd

starting to work with custom peak calling

317b83d

test commit

400895a

deleting functions that i don't need

22c4b90

saving the footprint before starting the new one

210bdda

background changing to mean + 10%, the score for a footprint is a mea…

54a5914

…n of all scores in this footprint

calculating the position with max score as the position in the middle…

c4f5bf3

… of first and last positions with max score

make save_footprint as a function on its own

b09d23c

writing to bed file

362cc54

adding the bonus information from the original bed file to the output…

b061f61

… footprints.bed

changing to the actual start and end position and not the relative on…

8c25200

…es within a peak

Basic Nextflow structure

36974c2

fixed db_channel for tomtom

0dbdf5b

adding a sorting function after the bed file was written to present i…

2d42086

…t nice for the user

adding of a logger, deleting of the unsorted file after the sorting

59a08fc

bed_to_fasta update

b4b972f

Merge branch 'motif_estiamtion' of https://github.molgen.mpg.de/looso…

77e40e3

…lab/masterJLU2018 into motif_estiamtion

motif estimation docu in nf

82c0c13

get best motif from meme

14fef9d

Merge branch 'dev' into motif_estiamtion

42a279b

added process to get best motif per meme-file

5a7b661

added uropa config

603c814

added process create_uropa_config

9f4e480

added scripts for part 1.2

87bbda0

Update: process overlap_with_known_TFBS

da77364

backup before changing to use a window for search

bce329b

changing the input parameters, creating a function for searching with…

1cd5bb1

…in a window (not working yet)

first try with window, the problem is that in some cases the window s…

88c1336

…lides not, i don't know why

the search with sliding window is done, it needs to be tested

f1f0988

basti and others added 29 commits December 11, 2018 12:52

data error fixed

5f849b8

error in output fixed

476c25d

Fixed small bug in output formatting for mm10/mm9

7357dc2

updated README

367dd33

minor bugfix

9026ad9

added T parameter for sorting

023bf56

removed parameter

8c939de

tfbsscan optional; minor fixes/changes

d6f9898

fixed yml-file

ff52b92

minor changes

9ff4281

Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU…

748fc0b

…2018 into dev

Update README.md

725d7c0

we do not need this env

5275f18

Update README.md

1c5f769

Update merge.R

7d05d05

check prameters; minor fixes

dc2363e

Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU…

6f0076b

…2018 into dev

Update README.md

1f45269

Update README.md

b69682a

Fixed bug in formatting (gff vs gtf). Converted feature description t…

ee03951

…o lowercase.

fixes

7aaf90c

resolve merge conflict

9318075

fix

63548bd

removed echo true from process

0d9892a

Readme formatted

6513638

$"motifs" falsch -> "$motifs" richtig :)

8a306b1

minor fix

fa5c838

Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU…

156e417

…2018 into dev

added info for FilterMotifs.stats

8669b3e

renewiegandt merged commit 614a0bb into master Dec 14, 2018

Dev #4

Dev #4

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renewiegandt commented Dec 14, 2018