Aggregating coverage values exon wise

Question

[Gene]

I have exon ranges, for example:

Chr_exon start - exon end

1_3774167-1_3774281

1_3775281-1_3775430

1_3782281-1_3782564

1_3784537-1_3784617

1_3786168-1_3786339

1_3789035-1_3789136

1_3800070-1_3800305

And also, I have, Coverage values for all positions,for example,

chr_position coverage value

1_3774167 175.6

1_3774168 175.6

1_3774169 175.6

1_3774170 175.6

1_3774171 175.6

1_3774172 175.6

1_3774173 175.6

1_3774174 175.6

Is it possible to aggregate them exon wise? For example, query by exon range (start-end), and find mean for all values in that exon/ range using unix functions or maybe python ? Thanks a lot in advance. I am a beginner, and sorry if question is stupid.

[German.M.Demidov]

Since I am a bioinformatician from 90s, I would write a script in R that would do it for me! It could be 20 lines of code. But I am sure there are tools for that.

[Gene]

Thank you for your response. I am not that familiar with R, but will try to code it then in Python.

Answer 1

[Kevin Blighe]

For starting, you may want to get these into standardised formats:

cat file1.txt 
1_3774167-1_3774281
1_3775281-1_3775430
1_3782281-1_3782564
1_3784537-1_3784617
1_3786168-1_3786339
1_3789035-1_3789136
1_3800070-1_3800305

sed 's/[_\\-]/\t/g' file1.txt | cut -f1,2,4 > file1.bed

cat file1.bed 
1   3774167 3774281
1   3775281 3775430
1   3782281 3782564
1   3784537 3784617
1   3786168 3786339
1   3789035 3789136
1   3800070 3800305


cat file2.txt 
1_3774167 175.6
1_3774168 175.6
1_3774169 175.6
1_3774170 175.6
1_3774171 175.6
1_3774172 175.6
1_3774173 175.6
1_3774174 175.6

sed 's/[_\\ ]/\t/g' file2.txt | awk '{print $1"\t"$2"\t"$2"\t"$3}' > file2.bed

cat file2.bed
1   3774167 3774167 175.6
1   3774168 3774168 175.6
1   3774169 3774169 175.6
1   3774170 3774170 175.6
1   3774171 3774171 175.6
1   3774172 3774172 175.6
1   3774173 3774173 175.6
1   3774174 3774174 175.6

After that, you may find a solution via BEDTools or via GenomicRanges in R. You will have to se rules about ho to summarise coverage per exon.

Kevin