Sequence from Around Max TSS

The sequence_from_region_around_max_tss tool returns the sequence of selected regions around the maxTSS.

Note

This tool requires bedtools to be installed.

Usage

Usage:

PolTools sequence_from_region_around_max_tss [-h] max_tss_file left right

Required Arguments	Description
Max TSS FIle	Bed formatted file containing the max TSSs you want to use to make the heatmaps. This file can be generated from the make_regions_file_centered_on_max_tss program with a region size parameter of 1.
Left	Left part of the region to get the sequence.
Right	Right part of the region to get the sequence.

Behavior

sequence_from_region_around_max_tss will print out a fasta formatted file containing the sequences.

For example:

$ head tQ_max_tss.bed
chr1    959255  959256  NOC2L   46      -
chr1    960632  960633  KLHL17  27      +
chr1    966521  966522  PLEKHN1 8       +
chr1    1000096 1000097 HES4    87      -
chr1    1000295 1000296 ISG15   12      +
chr1    1020119 1020120 AGRN    35      +
chr1    1074306 1074307 RNF223  10      -
chr1    1116106 1116107 C1orf159        9       -
chr1    1231971 1231972 SDF4    321     -
chr1    1232242 1232243 B3GALT6 174     +

$ PolTools sequence_from_region_around_max_tss tQ_max_tss.bed -5 5 > output.tmp
$ head output.tmp
>NOC2L
TGCACGCTTC
>KLHL17
CCGGCAGTCT
>PLEKHN1
TGTACGACTC
>HES4
CGCGCGCGGG
>ISG15
CCTCCGACAC