How to handle multiple overlap and choose closest one?
I have gtf file and i have disjointed exon file from DExSeq. I have to identify which exon is affected. for example my (i converted gtf to bed).
1 1400158 1400608 + ENSE000045454
1 1400158 1400544 + ENSE000045482
And i have my flattened exon bed file like this.
1 1400473 1400544 +
Since my exon can overlap with both coordinates of gtf , but i want to extract 1 1400158 1400544 + ENSE000045482 this one . How can i do this?
• 875 views
•
link
updated
by
Pierre Lindenbaum
•
written
by
PK •
•
written
by
PK •
1 answer
bedtools closest https://bedtools.readthedocs.io/en/latest/content/tools/closest.html
• 0 views
•
link
written
by
Pierre Lindenbaum
Log in to answer this question.
More posts like this
-
Dexseq non-stranded index error
written by bart •
-
How to plot that the certain exons are affected in the genebody?
written by PK •
-
How to extract intron counts from total RNA Sequencing?
written by PK •
-
Trouble finding exons in DEXseq
written by dan •
-
intersect between introns and the UTR/CDS bed files
written by Kai_Qi
-
genomic reads count
written by 13263617869xf •
-
Parse out exon for divergent primer design
written by 1769mkc
-
TCGA raw counts DexSeq
written by Newbie •
-
DEXSeq with cufflinks gtf file
written by Assa Yeroslaviz
-
Extract gene coordinates from GTF
written by int11ap1
