tsrFinder
The tsrFinder tool identifies transcription start regions from PRO-Cap, PRO-Seq, and related sequencing experiments.
This tsrFinder is a much quicker version (with few output modifications) of the previous two tsrFinders: one and
two.
Usage
Usage:
PolTools tsrFinder [-h] [-t [threads]]
seq_file window_size min_seq_depth
min_avg_transcript_length max_fragment_size
chrom_size_file
Required Arguments |
Description |
|---|---|
Sequencing File |
Bed formatted file from a sequencing experiment. |
Window Size |
The size of the TSRs to find. |
Min Seq Depth |
The minimum number of 5’ reads to be considered as a TSR. |
Min avg Transcript Length |
The minimum average transcript length will eliminate TSRs from sequencing artifacts. |
Max fragment size |
The maximum transcript length for a read to be included in tsrFinder analysis. |
Chrom size file |
A file containing the chromosome sizes. This can be optained using fetchChromSizes The hg38 chromsome size file can be found in the PolTools static directory. |
Optional Arguments |
Description |
|---|---|
-t, –threads |
Maximum number of threads. Default is the number of threads on the system. This program will not use more threads than twice the number of chromosomes in the chrom size file. |
Behavior
tsrFinder generate a file named the sequencing file plus the tsrFinder parameters and -TSR.bed. This file contains
the chromosome, left position, right position, the read sum, number of 5’ ends, strand, TSS left and right positions,
the TSS strength, and the position of the average TSS (weighted mean location).
For example:
$ head seq_file.bed
chr1 11981 12023 A00876:119:HW5F5DRXX:1:2168:2248:1407 255 -
chr1 13099 13117 A00876:119:HW5F5DRXX:1:2203:31403:26757 255 -
chr1 13356 13423 A00876:119:HW5F5DRXX:1:2151:15808:7827 255 -
chr1 13435 13477 A00876:119:HW5F5DRXX:1:2273:15781:19241 255 -
chr1 13739 13772 A00876:119:HW5F5DRXX:1:2256:29966:10520 255 -
chr1 13741 13773 A00876:119:HW5F5DRXX:1:2235:4101:11882 255 -
chr1 14178 14203 A00876:119:HW5F5DRXX:1:2115:8241:31422 255 -
chr1 14734 14768 A00876:119:HW5F5DRXX:1:2165:23764:2440 255 -
chr1 14988 15012 A00876:119:HW5F5DRXX:1:2219:16134:32784 255 -
chr1 18337 18362 A00876:119:HW5F5DRXX:1:2149:32054:31328 255 -
$ head hg38.chrom.sizes
chr1 248956422
chr2 242193529
chr3 198295559
chr4 190214555
chr5 181538259
chr6 170805979
chr7 159345973
chrX 156040895
chr8 145138636
chr9 138394717
$ PolTools tsrFinder seq_file.bed 20 20 30 600 hg38.chrom.sizes
$ head seq_file_20_20_30_600-TSR.tab
chr1 629421 629441 738 20 + 629431 629432 4 629431
chr1 629490 629510 2263 64 + 629494 629495 14 629500
chr1 629564 629584 13877 273 + 629571 629572 188 629572
chr1 629685 629705 939 21 + 629698 629699 6 629697
chr1 629708 629728 1701 43 + 629723 629724 12 629719
chr1 629740 629760 1911 63 + 629759 629760 21 629753
chr1 629919 629939 1219 32 + 629929 629930 6 629931
chr1 630666 630686 2277 44 + 630681 630682 21 630679
chr1 630824 630844 658 21 + 630828 630829 4 630834
chr1 630879 630899 2237 49 + 630893 630894 16 630890