Read Through Transcription

The read_through_transcription tool computes the coverage of 3’ ends of sequencing data around the 3’ end of features provided. This can be used to look at read through or runaway transcription by providing the gene body regions file from truQuant.

Note

This tool requires bedtools to be installed.

Usage and option summary

Usage:

PolTools read_through_transcription [-h] [-t [threads]]
                                           regions_filename tsr_file
                                           upstream_distance
                                           downstream_distance interval_size
                                           sequencing_files
                                           [sequencing_files ...]

Required Arguments

Description

Regions Filename

Bed formatted file containing all the genes to quantify (regions will be determined from the 3’ end of each region in this file.

TSR Filename

tsrFinder output file which will be blacklisted. Simply type no to not blacklist TSRs.

Upstream Distance

The number of base pairs to subtract from the left position.

Downstream Distance

The number of base pairs to add from the left position.

Interval Distance

The size of sub-regions to split the regions into.

Sequencing Files

Sequencing files to quantify separated by spaces.

Behavior

read_through_transcription will report the position relative to the 3’ end of the regions provided and the sum of the 3’ reads at that interval.

For example:

_images/read_through_transcription.png 

$ head regions_centered_on_max_tss.bed
chr1    959251  959261  NOC2L   46      -
chr1    960627  960637  KLHL17  27      +
chr1    966516  966526  PLEKHN1 8       +
chr1    1000092 1000102 HES4    87      -
chr1    1000290 1000300 ISG15   12      +
chr1    1020114 1020124 AGRN    35      +
chr1    1074302 1074312 RNF223  10      -
chr1    1116102 1116112 C1orf159        9       -
chr1    1231967 1231977 SDF4    321     -
chr1    1232237 1232247 B3GALT6 174     +

$ head seq_file-blacklisted_150_20_30_600-TSR.tab
chr1    199198  199348  759     22      +       199260  199261  2       199258
chr1    628994  629144  604     20      +       629092  629093  2       629110
chr1    629431  629581  17821   380     +       629571  629572  188     629551
chr1    629651  629801  6747    206     +       629764  629765  25      629740
chr1    629900  630050  2345    69      +       629929  629930  6       629955
chr1    630309  630459  1511    48      +       630437  630438  7       630406
chr1    630604  630754  3435    80      +       630681  630682  21      630690
chr1    630780  630930  4601    113     +       630893  630894  16      630873
chr1    630999  631149  2722    68      +       631136  631137  6       631116
chr1    631204  631354  2843    85      +       631294  631295  11      631287

$ 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     -

$ PolTools read_through_transcription seq_file-blacklisted_150_20_30_600-gene_body_regions.bed \
  seq_file-blacklisted_150_20_30_600-TSR.tab 1000 1000 100 seq_file.bed &
Position       seq_file.bed
-1000   1924
-900    1808
-800    1762
-700    1695
-600    1807
-500    1856
-400    2999
-300    3838
-200    2055
-100    1911
0       1809
100     1878
200     1977
300     1905
400     1885
500     1890
600     1894
700     1790
800     1718
900     1740