Bedfile format deeptools

Bedfile format deeptools

1

Hello everyone,

Using deeptools I am trying to plot the enrichment in Genebody and TSS for this we have to give one BED file region of interest in computeMatrix. I am bit confused about the format based on a thread in biostar TSS metaprofile using Deeptoolsbased on this thread I have converted my bed file trascript wise to gene wise can anyone suggest me is it a way of doing?

Original bed file transcript wise bed file

1   4970856 4971128 ENSMUSG00000085623  +
1   4971631 4971828 ENSMUSG00000085623  +
1   4973564 4976820 ENSMUSG00000085623  +
1   6213292 6213347 ENSMUSG00000090031  -
1   6214232 6214590 ENSMUSG00000090031  -
1   4879201 4880669 ENSMUSG00000062588  -
1   4880048 4880051 ENSMUSG00000062588  -
1   4880051 4880651 ENSMUSG00000062588  -
1   4880648 4880651 ENSMUSG00000062588  -

convert Gene wise bed file

1   4970856 4976820 ENSMUSG00000085623  +
1   6213292 6214590 ENSMUSG00000090031  -
1   4879201 4880669 ENSMUSG00000062588  -


Genome


DNA


Deeptools


ChIP-seq

• 59 views

A TSS is a transcript-level feature, so normally you would have a BED file with an entry for each transcript. Ideally the transcript ID would appear in column 4.


Login
before adding your answer.

Traffic: 2027 users visited in the last hour

Read more here: Source link